PART II

APPELLATE
PRACTICE,
PROCEDURE IN THE
COURT OF APPEALS,
COURT OF TAX
APPEALS, AND THE
SUPREME COURT

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 II. POST-JUDGMENT REMEDIES OTHER THAN APPEAL

Q: What are the differences between petitions for relief from judgments [Rule 38] and annulment of
judgments [Rule 47]?

A:

PETITION FOR RELIEF ANNULMENT OF JUDGMENTS

[RULE 38] [RULE 47]

DIRECTED AGAINST

Judgments and finals orders of either the —

1. MTC
2. RTC

WHERE FILED

Court that rendered the judgment or final 1. CA - for judgments of RTC; it has exclusive
order original jurisdiction over actions for
annulment of judgments (Sec. 1, Rule 47,
ROC, as amended)
2. RTC - for judgments of MTC (Sec. 10, Rule
47, ROC, as amended)

WHO CAN FILE

Only parties to the proceeding Any person adversely affected by the judgment or
final order

GROUNDS

(F-A-M-E) 1. Extrinsic fraud

1. Fraud 2. Lack of jurisdiction
2. Accident a. Over the subject matter
3. Mistake b. Over the person of the defendant
4. Excusable Negligence 3. Violation of Due Process

PRE-REQUISITE

It can be filed only when there are no other available adequate remedies or such adequate
remedies were not availed of

PERIOD TO FILE

Within sixty (60) days after the petitioner 1. Extrinsic fraud — the action must be filed
learns of the judgment, final order or within four (4) years from its discovery
proceeding AND not more them six (6) 2. Lack of jurisdiction or violation of due
months after such judgment or final order process — the action must be brought
was entered before the action is barred by laches or
estoppel

EFFECT OF GRANT

1. If petition for relief from the judgment, 1. If based on Extrinsic Fraud — The court,
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 final order or proceeding — Court upon motion, may order the trial court to try
shall set aside the judgment, final the case as if a motion for new trial was
order or other proceeding complained granted
of. The case then shall stand as if 2. If based on Lack of Jurisdiction or Violation
such judgment, final order or of Due Process — Court shall set aside the
proceeding had never been rendered, questioned judgment or final order and
issued or taken. The court shall then rendering the same null and void but the
proceed to hear and determine the judgment of annulment is without prejudice
case as if a timely motion for a new to the refiling of the original action in the
trial or reconsideration had been proper court.
granted by it
2. If petition for relief from denial of
appeal — Court shall set aside the
previous denial of the appeal and
shall give due course to the said
appeal. It shall then elevate the
records of the appealed case as if a
timely and proper appeal had been
made
Note: Since the judgment is already
final and executory, it is necessary for
the petitioner to apply for the
issuance of a writ of preliminary
injunction. Otherwise, the judgment
will be executed.

Q: What is the period of appeal under Rule

III. APPEALS IN CIVIL PROCEDURE: MODES 43?
OF APPEAL FROM JUDGMENTS OR FINAL A: The appeal shall be taken within fifteen (15)
ORDERS OF VARIOUS days from notice of the award, judgment, final
COURTS/TRIBUNALS order or resolution, or from the date of its last
publication, if publication is required by law for its
effectivity, or of the denial of petitioner’s motion
Q: When does Rule 43 apply?
for new trial or reconsideration duly filed in
A: This Rule shall apply to appeals from
accordance with the governing law of the court or
judgments or final orders of the Court of Tax
agency a quo. (Section 2, Rule 43)
Appeals and from awards, judgments, final orders
or resolutions of or authorized by any
Q: Does the Court of Appeals have jurisdiction
quasijudicial agency in the exercise of its
to review the Decisions in criminal and
quasi-judicial functions. (Section 1, Rule 43)
administrative cases of the Ombudsman?
(2006 Bar)
Q: What are cases not covered under Rule 43?
A: Yes, but only in administrative cases. In
A: This Rule shall not apply to judgments or final
administrative and disciplinary cases, appeals
orders issued under the Labor Code of
from the Ombudsman must be taken to the Court
Philippines. (Section 2, Rule 43)
of Appeals under Rule 43. Conversely, the
Supreme Court has exclusive appellate
Q: Where should you appeal under Rule 43?
jurisdiction over decisions of the Ombudsman in
A: An appeal under this Rule may be taken to the
criminal cases. (Lanting v. Ombudsman, G.R. No.
Court of Appeals within the period and in the
141426, May 6, 2005; Fabian v. Desierto, G.R.
manner herein provided, whether the appeal
No. 129742, September 16, 1998; Sec. 14, RA
involves questions of fact, of law, or mixed
6770)
questions of fact and law. (Section 1, Rule 43).

4
Note: Insofar as resolutions of the ombudsman 3. Under no other circumstances other than
on the criminal liability of the accused, the proper the limited grounds provided above may
remedy is to file a petition for certiorari under Rule parties appeal to the CA a CIAC arbitral
65 directly with the Supreme Court award.

Q: What is the remedy to assail an arbitral Petition for Review to CA under Rule 43 is no
award of the Construction Industry Arbitration longer applicable to arbitral awards of the
Commission? Construction Industry Arbitration Commission
A: (CIAC).
1. For appeals from CIAC arbitral awards (Ross Systems International, Inc. v. Global
that have already been filed and are Medical Center of Laguna, G.R. No. 230119, May
currently pending before the CA under 11, 2021)
Rule 43, the prior availability of the appeal
on matters of fact and law thereon applies. Q: What is the difference between Rule 45 and
This is only proper since the parties Rule 65?
resorted to this mode of review as it was A:
the existing procedural rules at the time of
RULE 45 RULE 65
filing, prior to the instant amendment.
Petition for review on Petition for certiorari
2. For future appeals from CIAC arbitral certiorari/appeal by
awards that will be filed after the certiorari
promulgation of this Decision:
a. If the issue to be raised by the Ordinary appeal Special civil action
parties is a pure question of law,
the appeal should be filed directly Directed against final Directed against
and exclusively with the Supreme judgment or final orders interlocutory orders or
Court through a petition for review since it is a mode of matters where no
under Rule 45. appeal appeal may be made
b. If the parties will appeal factual
issues, the appeal may be filed Decisions, final orders or Not an appeal but a
with the CA, but only on the limited resolutions of the CA, in special civil action
grounds that pertain to either a any case, i.e., regardless
challenge on the integrity of the of the nature of the
CIAC arbitral tribunal (i.e., action or proceedings
allegations of corruption, fraud, involved, may be
misconduct, evident partiality, appealed to the Supreme
incapacity or excess of powers Court by filing a petition
within the tribunal) or an allegation for review or appeal by
that the arbitral tribunal violated the certiorari.
Constitution or positive law in the
conduct of the arbitral process, The Court reviews errors Restricted to resolving
through the special civil action of judgment allegedly errors of jurisdiction
of a petition for certiorari under committed by the CA on and grave abuse of
Rule 65, on grounds of grave purely questions of discretion, not errors
abuse of discretion amounting to law. of judgment, and
lack or excess in jurisdiction. The generally, the subject
CA may conduct a factual review thereof are interlocutory
only upon sufficient and orders.
demonstrable showing that the
integrity of the CIAC arbitral
tribunal had indeed been Note: A petition for certiorari is unavailing if
compromised, or that it committed appeal remains a remedy. It cannot be resorted to
unconstitutional or illegal acts in for a lapsed appeal, especially if the failure to file
the conduct of the arbitration. a notice of appeal was attributable to the party
appealing.
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 If an assessment notice is sent without informing
Case law has it that a petition for certiorari filed the taxpayer in writing about the law and facts on
under Rule 65 has in more than one occasion, which the assessment is made, the assessment
treated by the Supreme Court as a petition for
is void (R.R. No. 18-2013, Sec. 3.1.3)
review on certiorari under Rule 45, provided that
the petition for certiorari was filed during the
reglementary period for filing a rule 45 petition, Comparing LOA vs LN
and contains sufficient allegations warranting The LOA gives notice to the taxpayer that it is
review of the findings of the court a quo by the under investigation for possible deficiency tax
court. assessment; at the same time it authorizes or
empowers a designated revenue officer to
V. PROCEDURE IN TAX CASES examine, verify, and scrutinize a taxpayer's books
and records, in relation to internal revenue tax
I. Administrative remedies liabilities for a particular period.” (CIR v. Lancaster
Philippines, Inc., G.R. No. 183408, July 12, 2017)
Requirement of a Letter of Authority for
Assessment Q: What are the requisites of a valid Letter of
Q: A company received a Letter Notice from Authority (LOA)?
the BIR assessing it for deficiency income tax A: The following are the requisites of a valid letter
due to a difference in the company’s sales as of authority:
per Financial Statement and its Income Tax 1. It must be Issued by the proper
Return. The company failed to reply to the LN. approving official. The approving
The BIR sent a Preliminary Assessment Notice official depends on the investigating
and subsequently a Final Letter of Demand for office:
the payment of the income tax. The company a. Regional Director (RD);
avers that BIR is not allowed to do so without b. Assistant Commissioner-Large
a Letter of Authority. The company hired you Taxpayer Service (ACIR-LTS) –
as their lawyer to represent them before BIR. LTS and its Divisions;
What legal defenses can you raise against the c. Deputy Commissioner-Legal
assessment? and Inspection Group –
A: First, I will question the validity of the Enforcement Service and its
assessment that the FAN/DL must be issued on Divisions; and
account of or covered by a validly issued letter of d. CIR or any authorized official –
authority (RMC No. 75-2018) (Medicard Phil Inc. Task Force and Special Teams
v. CIR, G.R. No. 222743, April 5, 2017) (RMO No. 44-10);
2. It must Not contain any
In this case, there was no valid LOA that was manually-written character, notation or
issued before the issuance of the FAN/Demand erasure (RMO No. 44-10);
Letter. It is evident from the foregoing that a grant 3. It must Cover only one (1) taxable
of authority is indispensable before a revenue year, except in tax fraud cases
officer can conduct an examination or authorized by the CIR or Deputy
assessment and that the absence thereof results Commissioner and excise tax cases
to the nullity of the examination or the tax (RMO No. 44-10); and
assessment itself. (Vesta Property Holdings, Inc. 4. It must be served to the taxpayer
v. CIR, CTA En Banc Nos. 1847 & 1848, within thirty (30) days (RAMO No.
September 27, 2019) 1-00).

Q: Can BIR issue an LOA for unverified prior

6
years? Statute of Limitations?
A: No. The requirement to specify the taxable A: The requisites are as follows:
period covered by the LOA is simply to inform the 1. The waiver must be in the proper Form
taxpayer of the extent of the audit and the scope prescribed by RMO No. 20-90;
of the revenue officer’s authority. Without this rule, 2. The waiver must be Signed by the
a revenue officer can unduly burden the taxpayer taxpayer himself or his duly authorized
by demanding random accounting records from representative. In the case of a
random unverified years which may include corporation, the waiver must be signed
documents from as far back as ten years in cases by any of its responsible officials;
of fraud audit (CIR v. De La Salle University, Inc., 3. The waiver should be duly Notarized;
G.R. No. 196596, 198841, & 198941, November 4. The CIR or the revenue official
9, 2016). authorized by him must sign the
waiver indicating that the BIR has
Waiver of Statute of Limitations Accepted and agreed to the waiver;
CIR v. Systems Technology Institute: Estoppel 5. Both the Date of execution by the
does not apply as an exception to the statute of taxpayer and Date of acceptance by
limitations the Bureau should be before the
Q: BIR audited and examined the books of expiration of the period of prescription
XYZ Corporation for the taxable year 2003. In or before the lapse of the period
three instances, waivers were executed by agreed upon in case a subsequent
XYZ Corporation extending the prescriptive agreement is executed; and
period for the taxable year 2003. In all those 6. The waiver must be executed in Three
instances, there was no notarized written copies, the original copy to be
authority from the BOD of XYZ Corporation attached to the docket of the case, the
regarding the signatory of the waivers. CTA second copy for the taxpayer and the
canceled the assessment finding that the third copy for the Office accepting the
waivers were defective for failure to comply waiver (CIR v. Systems Technology
with RMO 20-90 and RDAO 05-01, rendering Institute, Inc., G.R. No. 220835, July
the assessment barred by prescription. CIR 26, 2017, Caguioa Case).
asserts that the waivers executed are valid
and that the active participation of XYZ Note: The waiver may be, but not necessarily, in
Corporation in the administrative investigation the form prescribed by RMO No. 20-90 or
amounts to estoppel that the prescription can Revenue Delegation Authority Order (RDAO) No.
no longer be invoked. Is the contention 05-01.
correct?
A: No. The doctrine of estoppel cannot be applied The taxpayer’s failure to follow the aforesaid
as an exception to the statute of limitations on the forms does not invalidate the executed waiver for
assessment of taxes considering that BIR is as long as the following are complied with:
bound to follow a strict requirement in the 1. The Waiver of the Statute of Limitations
execution of a proper waiver. The RMO 20-90 under Section 222 (b) and (d) shall be
and RDAO 05-01 which were issued by BIR itself executed before the expiration of the
should prevail over the fault of BIR. Having period to assess or to collect taxes. The
caused the defects in the waivers, the BIR must date of execution shall be specifically
bear the consequence. It cannot simply shift the indicated in the waiver;
blame to the taxpayer (CIR v. Systems 2. The waiver shall be signed by the
Technology Institute, G.R. No. 220835, July 26, taxpayer himself or his duly authorized
2017, Caguioa) representative. ln the case of a
Q: What are the requisites of the waiver of corporation, the waiver must be signed by
7
 any of its responsible officials; Limitation.
3. The expiry date of the period agreed upon
to assess/collect the tax after the regular Prescription Periods for Assessment and
three-year period of prescription should be Collection by BIR
indicated (RMO No. 14-2016). Q: XYZ Corp received LOA for taxable year
2010 on Oct 30, 2012. PAN was issued on Nov
Note: In the case of CIR v. Systems Technology 28, 2014 which was replied to by the Corp on
Institute, Inc. (G.R. No. 20835, dated July 26, December 15, 2014. CIR sent out the FAN or
2017), the Supreme Court ruled that the FLD on December 12, 2014. No protest was
requirements laid down by RMO No. 20-90 and filed by the corporation, hence, CIR issued
RDAO No. 05-01 are mandatory and must strictly FDDA on March 3, 2015. The company filed
be followed; which is in conflict with the liberality with CIR a request for reconsideration on
and relaxed guidelines of RMO No. 14-2016. The March 30, 2015 which was denied by CIR on
Supreme Court in this case did not touch upon February 4, 2020.
RMO No. 14-2016 nor mentioned the same for Corporation filed a Petition for review before
this RMO was raised by neither party CTA where it alleges that CIR’s right to collect
taxes has already been prescribed on
II. Protest in the assessment December 12, 2019 or five years from date of
FAN or FLD on December 12, 2014.
Q: What is the effect of failure to file protest?
A: If the taxpayer fails to file a valid protest
Has CIR’s right to collect taxes already
against the FLD/FAN within thirty (30) days from
prescribed?
date of receipt thereof, the assessment shall
A: Yes, the CIR's right to collect taxes had
become final, executory, and demandable. No
prescribed. The three-year, and not the five-year,
request for reconsideration or reinvestigation shall
period applies to this case. Here, given that the
be granted (R.R. No. 12-99, Sec. 3.1.4, as
subject assessment was issued within the
amended by R.R. No. 18-2013).
three-year ordinary prescriptive period to assess,
the CIR had another three years to initiate the
Q: What is the difference between a request
collection of taxes by distraint or levy or court
for reinvestigation and a request for
proceeding. Accordingly, since the FAN/FLD was
reconsideration in a protest to FAN?
mailed on December 12, 2014, the CIR had
A: In requests for reinvestigation, the taxpayer
another three years reckoned from said date, or
can still submit additional supporting documents
until December 12, 2017, to enforce collection of
of the submitted protest within 60 days from the
the assessed deficiency taxes. Verily, prescription
date of filing of his letter of protest (R.R. No.
had already set in when the CIR initiated its
18-2013, Sec. 3.1.4). While a request for
collection efforts only in 2020. The Court also
reconsideration, the 60-day period shall not apply
notes that regardless of which period to apply,
and BIR is to re-evaluate the assessment based
i.e., five years as determined by the CTA Division
on existing records without any submission of
or three years, the CIR's collection efforts were,
additional documents (R.R. No. 12-99, Sec. 3.1.4,
as they are, barred by prescription
as amended by R.R. No. 18-2013).
(Commissioner of Internal Revenue v. Court of
Tax Appeals Second Division, G.R. No. 258947,
Reinvestigation will toll the Statute of Limitations
[March 29, 2022], Caguioa Case)
because a reinvestigation which entails reception
of additional evidence will take more time than
reconsideration (CIR v. Philippine Global
Communications, G.R. No. 167146, October 31,
2006). Reconsideration will not toll the Statute of III. Judicial remedies for judicial appeals (from
8
 BIR to the SC) power to interpret the NIRC. Is the Petition for
Certiorari under Rule 65 proper?
Q: What is the appropriate civil action in A: No. Certiorari under Rule 65 will only lie if
assailing interlocutory orders of CTA there is no appeal, or any other plain, speedy and
Division? adequate remedy in the ordinary course of law
A: Rule 65 before the SC. Jurisdiction is against the assailed issuance of the CIR. The
conferred by law and nothing under RA 9282 plain, speedy and adequate remedy expressly
confers certiorari jurisdiction upon the CTA en provided by law is an appeal of the assailed RMO
Banc over interlocutory orders of the CTA (CIR v with the Secretary of Finance under Section 4 of
CTA GR Nos 203054-55, July 29, 2015) the NIRC. Hence, C violated the doctrine of
hierarchy of courts when it directly filed its Petition
Q: Upon receipt of a decision or ruling of the under Rule 65 in the SC (Confederation for Unity,
CTA en Banc, can the taxpayer file a petition Recognition and Advancement of Government
for review before SC? Employees v. Commissioner, Bureau of Internal
A: Yes. The taxpayer may file with the Supreme Revenue, G.R. Nos. 213446 & 213658; July 03,
Court a verified petition for review on certiorari 2018, Caguioa Case).
within 15 days from receipt of the decision or
ruling pursuant to Rule 45 of the ROC (RRCTA, Q: Assuming C violated the doctrine of
Rule 16, Sec. 1). hierarchy of courts, may the SC take
cognizance of the case?
Q: What is the effect of the appeal filed with A: Yes. A direct invocation of the SC’s jurisdiction
SC in relation to the pending motion for should only be allowed when there are special,
reconsideration or new trial to the CTA en important and compelling reasons clearly and
Banc? specifically spelled out in the petition. In this case,
A: Pending motion in the CTA en Banc shall be the petition assails the validity of the actions of
deemed abandoned. the CIR that affect thousands of employees in the
different government agencies and
Q: CIR issued RMO No. 23-2014 which instrumentalities. Hence, despite the procedural
consolidated the responsibilities of the public infirmities of the petition that warrants its outright
sector to withhold taxes on its transactions as dismissal, the SC may take cognizance of, and
a customer (on its purchases of goods and accordingly act on the petition to promote the vital
services) and as an employer (on interest of justice (Confederation for Unity,
compensation paid to its officials and Recognition and Advancement of Government
employees) under the NIRC. C, an Employees v. Commissioner, Bureau of Internal
organization of government employees filed a Revenue, G.R. Nos. 213446 & 213658; July 03,
petition for certiorari, prohibition and/or 2018, Caguioa Case).
mandamus under Rule 65 with the Supreme
Court (SC) seeking to nullify some of the Q: When may a petition for review on
provisions of the RMO for being ultra vires certiorari be taken in civil cases?
and violative of the equal protection clause A: Any party adversely affected by a decision or
and the fiscal autonomy enjoyed by ruling of the CTA en banc may file with the
government agencies and that its Supreme Court a verified petition for review on
certiorari within 15 days from receipt thereof
implementation results in diminution of
pursuant to Rule 45 of the 1997 Rules of Court
benefits of government employees, a violation (RRCTA, Rule 16, Sec. 1).
of Article 100 of the Labor Code. CIR and
Secretary of Finance counter that the petition
is barred by the doctrine of hierarchy of
courts and it was issued pursuant to the CIR’s Q: When may a petition for review on

9
certiorari be taken in criminal cases? (September 28, 2007) from the BIR for an
A: A party adversely affected by a decision or informal conference. It was found that XYZ
ruling of the CTA en banc may appeal therefrom has tax deficiencies. On January 14, 2008,
by filing with the Supreme Court a verified petition
XYZ received FAN. On January 24, 2008, XYZ
for review on certiorari within 15 days from receipt
of a copy of the decision or resolution, as filed a protest to the FAN with the RD. On
provided in Rule 45 of the Rules of Court. If such August 14, 2008, it elevated its protest to CIR
party has filed a motion for reconsideration or for claiming that no action was taken thereon. On
new trial, the period herein fixed shall run from March 11, 2009, XYZ filed a Petition for Review
the party’s receipt of a copy of the resolution alleging BIR’s inaction in its protest. The CTA
denying the motion for reconsideration or for new 1st Division ruled that the Petition for Review
trial (RRCTA, Rule 16, Sec. 1).
was filed beyond the reglementary period for
appeal depriving the court of jurisdiction. The
IV. Jurisdiction of the CTA
(Particularly what is appealable to the CTA) CTA en Banc affirmed the decision. Did XYZ
correctly appeal?
Q: LLL was issued an FLD/FAN, assessing it A: No. A textual reading of Section 3.1.5 of R.R.
for deficiency expanded withholding tax No. 12-99 gives a protesting taxpayer only three
(EWT) and deficiency fringe benefits tax (FBT). options:
After the taxpayer protested the assessment,
the BIR issued the final decision on disputed 1. If the protest is wholly or partially denied
assessment (FDDA) still finding the taxpayer by the CIR or his authorized
liable, but the amounts were different from representative, then the taxpayer may
those stated in the FAN without stating the appeal to the CTA within 30 days from
factual bases. LLL contends that a void FDDA receipt of the whole or partial denial of the
will lead to a void assessment because the protest.
FDDA ultimately determines the final tax 2. If the protest is wholly or partially denied
liability of a taxpayer. Will the invalidity of the by the CIR’s authorized representative,
FDDA ipso facto render the assessment void? then the taxpayer may appeal to the CIR
A: No. A decision of the CIR on a disputed within 30 days from receipt of the whole or
assessment differs from the assessment itself. partial denial of the protest.
Hence, the invalidity of one does not necessarily 3. If the CIR or his authorized representative
result to the invalidity of the other — unless the failed to act upon the protest within 180
law or regulations otherwise provide. What is days from submission of the required
appealable to the CTA is the “decision” of the CIR supporting documents, then the taxpayer
on disputed assessment and not the assessment may appeal to the CTA within 30 days
itself. An FDDA that does not inform the taxpayer from the lapse of the 180-day period.
in writing of the facts and law on which it is based
renders the decision void. Therefore, it is as if When XYZ filed its petition before the CTA, it is
there was no decision rendered by the CIR. It is clear that XYZ failed to make use of any of the
tantamount to a denial by inaction by the CIR, three options described above. XYZ ‘s petition
which may still be appealed before the CTA and before the CTA may only be made after a whole
the assessment evaluated on the basis of the or partial denial of the protest by the CIR or the
available evidence and documents (CIR v. CIR’s authorized representative. XYZ still should
Liquigaz Philippines Corp., G.R. Nos. 215534, have waited for the RD’s decision until October
April 18, 2016). 27, 2008, or 180 days from April 30, 2008. XYZ
then had 30 days from October 27, 2008, or until
November 26, 2008, to file its petition before the
CTA. XYZ, however, did not make use of the third
Q: XYZ received a Post Reporting Notice option. XYZ did not file a petition before the CTA
10
on or before November 26, 2008. When XYZ filed due from ABC Corp., the BIR issued a Formal
its petition before the CTA on March Demand Letter. After being served with a
11, 2009, there was still no denial of XYZ’s protest Warrant of Distraint and/or Levy to enforce the
by either the RD or the CIR. Therefore, under the collection of taxes, ABC Corp. appealed to the
first option, XYZ’s petition before the CTA had no BIR. ABC Corp. opted to wait for the decision
cause of action because it was prematurely filed of the CIR, and hence, failed to appeal to the
(Philippine Amusement and Gaming Corporation CTA within 30 days from the lapse of the
v. Bureau of Internal Revenue, G.R. No. 208731, 180-day period. If the CIR fails to act on the
January 27, 2016). appeal by ABC Corp. within 180 days, will the
assessment become final and executory?
Q: XYZ Corporation upon receipt of the FDDA A: No. In case of the inaction of the CIR on the
after failing to protest the FAN arising from a protested assessment, the taxpayer has two
valid assessment, filed a motion for options, either: (1) file a petition for review with
reconsideration with CIR alleging prescription the CTA within 30 days after the expiration of the
on the collection of the assessed deficiency 180-day period; or (2) await the final decision of
taxes as ground for cancellation of the the CIR on the disputed assessment and appeal
assessment. CIR denied this motion. Hence, such final decision to the CTA within 30 days after
XYZ Corporation filed a Petition for Review the receipt of a copy of such decision.
before the CTA. The CIR claims that the
company’s failure to file a valid protest to the These options are mutually exclusive and resort
FAN/FLD rendered the assessment against it to one bars the application of the other.
already final, executory, and demandable. As Considering that ABC Corp. opted to await the
such, the assessments are not subject to final decision of the CIR on the protested
judicial scrutiny, as it is already beyond the assessment, it then has the right to appeal such
CTA Division's jurisdiction. Is the CIR correct? final decision to the CTA by filing a petition for
A: No. The CIR's argument must fail in light of review within thirty days after receipt of a copy of
Section 7 (a) (1) of Republic Act No. (RA) 1125, such decision or ruling, even after the expiration
as amended by RA 9282, which confers upon the of the 180-day period fixed by law for the CIR to
CTA the jurisdiction to decide not only cases on act on the disputed assessments (Lascona Land,
disputed assessments and refunds of internal Co., Inc. v. CIR, G.R. No. 171251, March 5,
revenue taxes, but also "other matters" arising 2012).
under the NIRC. To be sure, the fact that an
assessment has become final for failure of the Q: Does CTA have jurisdiction over all tax
taxpayer to file a protest within the time allowed disputes involving two government agencies
only means that the validity or correctness of the notwithstanding procedures laid down in PD
assessment may no longer be questioned on 242?
appeal. However, the validity of the assessment A: Yes. Requiring all disputes between
itself is a separate and distinct issue from the government entities on tax-related matters to be
issue of whether the right of the CIR to collect the lodged before the Secretary of Justice (or the
validly assessed tax has prescribed. This issue of Solicitor General) will not only be at variance with
prescription, being a matter provided for by the the Supreme Court En Banc's pronouncement in
NIRC, is well within the jurisdiction of the CTA to Banco De Oro (that the law intends the CTA to
decide (Commissioner of Internal Revenue v. have exclusive jurisdiction to resolve all tax
Court of Tax Appeals Second Division, G.R. No. problems) but will also encourage multiplicity of
258947, [March 29, 2022], Caguioa Case) suits and split jurisdiction.
Under Section 218 of the 1997 NIRC, "[n]o court
shall have the authority to grant an injunction to
Q: Pursuant to the finding of deficiency taxes restrain the collection of any national internal
11
revenue tax, fee or charge." By way of exception,
Section 11 of RA 1125, as amended, gives the
CTA the authority to suspend collection of internal
revenue taxes, fees or other charges when, in its
opinion, such collection may jeopardize the
interest of the Government and/or the taxpayer.
Only the CTA which has the authority to order the
suspension of collection internal revenue taxes in
disputed assessment cases. Unmistakably, there
will be split jurisdiction and multiplicity of suits if
government entities are mandated to seek
resolution of their tax disputes before the
Secretary of Justice (or the Solicitor General)
while the incidental matter of suspending the
collection of taxes would have to be secured from
another tribunal, i.e.,the CTA. This kind of
arrangement is certainly anathema to an orderly
administration of justice. (Davao City Water
District v. Commissioner of Internal Revenue,
C.T.A. Case Nos. 9138, 9139, 9140, 9141, 9142
& 9143, [May 6, 2022])

Q: Can the acting Collector of Customs file a

notice of appeal from the decision of the
Commissioner of Customs to the CTA?

A: No.Under RA No. 1125, the right to appeal

from decisions or rulings of officials is allowed
only to persons, associations or corporations
adversely affected by the same, and well knowing
the connotation of the legal maxim “inclusion
unius est exclusion alterius”, the Government is
certainly not one of them (Acting Collector of
Customs v. CTA, G.R. No. L-8811, October 31,
1957).

The Court held that as the Commissioner of

Customs is part of the Government, the remedy
against his decisions should be sought
administratively rather than in the judiciary.

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