G.R. No. 246379 - Commissioner of Internal Revenue vs. Dohle Shipmanagement Philippines Corporation

On March 31, 2014, Dohle Shipmanagement Philippines Corporation (Dohle) filed an application for refund or issuance of a tax credit certificate (TCC) for unutilized input Value-Added Tax (VAT) covering the four quarters of calendar year 2012.
On July 28, 2014, Dohle submitted additional documents to support its application.
The Commissioner of Internal Revenue (CIR) took no action on Dohle’s administrative claim.
Dohle filed a petition for review before the Court of Tax Appeals (CTA) Second Division on December 23, 2014, docketed as CTA Case No. 8960.

The CTA Second Division, in a decision dated December 16, 2016, partially granted Dohle's refund claim for PHP 7,196,472.58 representing unutilized excess input VAT attributable to its zero-rated sales.
The CTA found Dohle’s judicial claim timely filed within the 120+30-day periods under Section 112(C) of the National Internal Revenue Code of 1997, as amended, commencing from the date Dohle submitted complete supporting documents.
The CIR moved for reconsideration, challenging the probative value of Dohle’s documents, but the motion was denied by the CTA Special Second Division on May 22, 2017.

The CIR elevated the case to the CTA En Banc, arguing (a) Dohle’s invoices and receipts did not comply with legal requirements, and (b) the documents were hearsay with no probative value.
The CTA En Banc, in a decision dated July 26, 2018, denied the CIR’s petition for review and affirmed the Second Division's findings, holding that CIR failed to rebut the factual findings.
CIR’s motion for reconsideration before the CTA En Banc was denied on April 1, 2019.

CIR filed the present petition, contending that Dohle’s judicial claim was filed beyond the 120+30-day prescriptive periods under Section 112 of the 1997 Tax Code.
CIR relied heavily on the Supreme Court ruling in Pilipinas Total Gas, Inc. v. CIR, arguing the 30-day period to submit supporting documents started from the filing date of administrative claim and that the judicial claim filed in December 2014 was late.

Dohle maintained that the 120-day period for CIR to act begins only upon submission of complete documents and the 30-day judicial appeal period runs from the lapse of this 120-day period.
Dohle argued the CIR never notified any inadequacy of documents within the 30-day period following the administrative claim filing.

Section 112 of the 1997 Tax Code and subsequent amendments prescribe the timeframes for filing and processing VAT refund claims and judicial appeals.
CIR's Revenue Memorandum Circular (RMC) No. 49-2003 provides taxpayers 30 days to submit complete documents upon notice of insufficiency; otherwise, the CIR has 120 days to decide from submission of complete documents.
Subsequent Supreme Court decisions, especially Pilipinas Total Gas, clarified that the 120-day period to act on the claim runs from the submission of complete documents, with the taxpayer having the right to determine when they are complete, absent notice of insufficiency from the CIR.
The Court also discussed newer regulations effective after June 11, 2014 and TRAIN Law amendments effective January 1, 2018, but the present case involves claims filed before June 11, 2014, so older rules apply.

Whether Dohle’s judicial claim for VAT refund was filed timely within the prescriptive periods under Section 112 of the 1997 Tax Code.