G.R. No. 244154 - Zuellig-Pharma Asia Pacific Ltd. Phils. ROHQ vs. Commissioner of Internal Revenue

Zuellig-Pharma Asia Pacific Ltd. Phils. ROHQ (Zuellig-PH), a regional operating headquarters of a Hong Kong-based foreign corporation, is the petitioner.
The petitioner sought a refund or issuance of a tax credit certificate amounting to ₱39,931,971.21, representing excess and unutilized input VAT for calendar year (CY) 2010.

For CY 2010, Zuellig-PH timely filed its Quarterly VAT Returns (BIR Form No. 2550-Q) on April 22, July 21, October 20, 2010, and January 20, 2011.
On February 15, 2011, Zuellig-PH amended its Quarterly VAT Returns for all four quarters.
On February 17, 2011, the petitioner filed an administrative claim for refund with the BIR RDO No. 49, attaching BIR Form No. 1914.

The BIR issued Letter of Authority (LOA) No. eLA201000037096 on March 3, 2011, authorizing the examination of Zuellig-PH’s books and records for CY 2010.
On June 29, 2011, the BIR sent a written request asking for supporting documents regarding the administrative refund claim.
Zuellig-PH complied by submitting its records on July 5, 2011.
Thereafter, the BIR made additional verbal requests for further documents between 2012 and 2014, to which Zuellig-PH responded by submitting letters on May 8, 2012; July 25, 2012; December 6, 2012; and September 11, 2013.

On February 4, 2014, Zuellig-PH’s claim was transferred to the BIR Assessment Service and assigned to RO William P. Manzanares, Jr.
Due to processing delays, Zuellig-PH sent a letter on March 5, 2014, to Commissioner Kim S. Jacinto-Henares requesting prompt resolution.
The BIR, through Deputy Commissioner Nelson M. Aspe (letter dated March 12, 2014), explained that refund applications are processed on a “first-in-first-out” basis and assured that the claim would be processed within the statutory 120-day period provided all documents were submitted.
RO Manzanares later requested the resubmission of additional documents, and on April 29, 2014, Zuellig-PH confirmed that it had “already submitted the complete documents” supporting its refund claim.
Notably, the 120-day period to decide the refund was thus deemed to have started on April 29, 2014. When this period lapsed (August 27, 2014) without action from the BIR, Zuellig-PH then filed its judicial claim on September 25, 2014.

The BIR argued that the petition was filed out of time because the administrative claim should have been acted upon within 120 days starting from an earlier date (specifically, June 29, 2011, when the initial written request was issued).
According to the BIR, the petitioner had 30 days from the earlier lapse (stated to be in early December 2011) to file a judicial claim, which Zuellig-PH did not do until September 25, 2014.
The CTA-Second Division, in its decision dated March 9, 2017, upheld the BIR’s argument and dismissed the petition for being filed out of time.

After the dismissal by the CTA-Second Division, Zuellig-PH moved for reconsideration, arguing that the BIR’s repeated representations (both written and verbal) had induced it to believe that its submission was complete and its claim would be processed within the required period.
The motion for reconsideration was denied by the CTA-Second Division in a May 9, 2017 Resolution.
Zuellig-PH then elevated the matter to the CTA En Banc, which in a Decision dated January 21, 2019, affirmed the CTA-Second Division’s reliance on the ruling in Pilipinas Total Gas regarding the reckoning of the 120-day period.

The Supreme Court (Second Division) granted the petition for review, finding that the petition was meritorious.
The Court determined that the proper reckoning of the 120-day period for the BIR to act should be from the petitioner’s submission of complete documents (i.e., the April 29, 2014 letter), not from the initial written request issued on June 29, 2011.
The Court also held that the government cannot be estopped merely by referencing the general principle that errors by government agents do not typically estop the government, noting that injustice would result if Zuellig-PH were penalized.

Whether Zuellig-PH’s judicial claim for refund was filed within the time prescribed by law given the multiple requests and submissions of documents.
Determining the proper starting point for the 120-day period for the BIR to act on an administrative claim for VAT refund—whether it should be reckoned from the date of the initial written request (June 29, 2011) or from the date when the taxpayer submitted the complete documents (April 29, 2014).

Whether the taxpayer should be estopped from arguing timeliness due to the BIR’s repeated verbal and written requests for additional documents.
The role of the taxpayer’s reliance on government representations in establishing that its submission was complete and timely.

Whether the principles established in Pilipinas Total Gas regarding the submission of complete documents and the reckoning of the 120-day period are applicable to Zuellig-PH’s case.