When to file an MR for tax appeals cases
By: Atty. Raida Argeli G. Grefiel on October 30,2025
WHEN filing court cases, litigants should ensure their actions are brought before the proper forum, and all jurisdictional requirements complied with. The jurisdiction of the courts over the subject matter, or the courts’ power to hear and decide a case, is conferred by law and not by the parties.
For the Court of Tax Appeals (CTA), the scope of its jurisdiction and the procedural requirements governing the filing and appeal of cases are defined under the Revised Rules of the Court of Tax Appeals (RRCTA), as amended.
Under the RRCTA, a party intending to appeal a decision of a CTA Division to the CTA En Banc must first file a motion for reconsideration or a motion for new trial with the Division that rendered the decision. That is a requirement before the CTA En Banc acquires jurisdiction over a case appealed to it from the CTA Division. Otherwise, the case should be dismissed for the CTA En Banc’s lack of jurisdiction.
Following the filing of a motion for reconsideration or new trial before the CTA Division, the court may amend its own decision. As defined under the RRCTA, an amended decision is any action modifying or reversing a decision of the CTA Division or En Banc. It is important to note, however, that the filing of a second motion for reconsideration or new trial of a decision is prohibited and does not toll the running of the period to appeal.
This raises the question: When is it proper to file or not to file a motion for reconsideration or new trial against an amended decision?
Petition for refund
In the recent case of the Commissioner of Internal Revenue (CIR) v. Halliburton Worldwide Limited-Philippine Branch (CTA EB No. 3070) (the “Halliburton case”) the CTA in Division partially granted the taxpayer’s Petition for Refund of excess input value-added tax (VAT) worth P4,382,813.67 through its original Decision.
After the taxpayer filed a Motion for Partial Reconsideration, the CTA Division issued an Amended Decision, admitting the original carbon pink and white copies of the taxpayer’s receipts (which had been considered unreadable in the original Decision), resulting in an increased refund of P26,612,491.76.
Instead of filing a motion for reconsideration or a motion for new trial against the Amended Decision, the CIR filed before the CTA En Banc a Motion for Extension of Time to File Petition for Review and, subsequently, a Petition for Review assailing the grant of the refund in favor of the taxpayer.
In ruling that it lacked jurisdiction over the Petition for Review, the CTA En Banc explained that, pursuant to the RRCTA, the CIR should have first filed a motion for reconsideration or a motion for new trial with the CTA Division against the Amended Decision before elevating the case to the CTA En Banc.
In the previous case of Asiatrust Development Bank v. CIR, (G.R. No. 201530 & 201680-81), the Supreme Court (SC) held that an amended decision is a new and different decision. Thus, the rule on the filing of a motion for reconsideration or new trial applies to amended decisions.
However, it should be noted that in the 2021 Supreme Court case of CIR v. Commission on Elections (G.R. Nos. 244155 & 247508) (the “Comelec case”), the SC explained that not all amended decisions require the filing of a motion for reconsideration or new trial. If it merely clarifies the earlier ruling, such as by correcting a typographical error, then the amended decision is not a new one. Thus, it is not a proper subject of a motion for reconsideration or new trial.
To illustrate, in the Comelec case, the amended decision merely corrected the dispositive portion to conform with the original decision. Instead of directing the taxpayer to pay the full amount of P49,082,867.69 (representing the deficiency basic withholding tax plus deficiency interest), the amended decision clarified that the taxpayer was liable only for P30,645,542.62, excluding the deficiency interest as explained in the body of the original decision.
Reevaluation, modification
On the other hand, if the amended decision is a result of a reevaluation of the parties’ allegations, or reconsideration of new and/or existing evidence that were not considered and/or previously rejected in the original decision, then the modification is substantial and should be challenged through a motion for reconsideration or a new trial before the CTA Division that rendered the amended decision.
As in the Halliburton case, the Amended Decision arose from the admission and reevaluation of the taxpayer’s evidence, which led to a higher refund.
In summary, clarifications or minor corrections do not require the filing of a motion for reconsideration or a new trial. But substantial modifications arising from a reevaluation of evidence must be challenged before the CTA Division that issued the amended decision.
Raida Argeli G. Grefiel is an Associate of Mata-Perez, Tamayo & Francisco (MTF Counsel). This article is for general information only and is not a substitute for professional advice where the facts and circumstances warrant. If you have any question or comment regarding this article, you may email the author at info@mtfcounsel.com or visit MTF website at www.mtfcounsel.com
The article was published at the More to Follow Column at The Manila Times on October 30, 2025. Please see this link.