G.R. No. 192173 - Commissioner of Internal Revenue vs. Standard Chartered Bank

On June 24, 2004, the Commissioner of Internal Revenue (petitioner) issued a Formal Letter of Demand and Assessment Notices against Standard Chartered Bank (respondent) covering deficiency income tax, final income tax on Foreign Currency Deposit Unit (FCDU), withholding tax on compensation (WTC), expanded withholding tax (EWT), and final withholding tax (FWT) for taxable year 1998, totaling approximately ₱33,326,211.37 including increments.
Respondent received the demand on July 14, 2004.

On August 12, 2004, respondent filed a letter-protest challenging the assessments and requested their withdrawal.
Petitioner did not resolve the protest.
Due to inaction from the petitioner, on March 9, 2005, respondent filed a Petition for Review before the Court of Tax Appeals (CTA).

On October 14, 2005, respondent filed a Motion for Leave to Serve Supplemental Petition, citing partial payments made via BIR’s Electronic Filing and Payment System (eFPS) for deficiency WTC (₱124,967.73) and FWT (₱139,713.11).
The supplemental petition sought full credit for these payments, reducing the contested amount to ₱33,076,944.18, now covering only deficiency income tax, final income tax on FCDU, and EWT.
The CTA granted the motion and admitted the supplemental petition on December 12, 2005.

Respondent presented testimony and documentary evidence; petitioner likewise presented witnesses and exhibits.
After filing memoranda, the case was submitted for decision on November 12, 2008.

On February 27, 2009, the CTA in Division ruled that the assessment was void for being issued beyond the three-year reglementary period, as the waivers of the statute of limitations were invalid for non-compliance with RMO No. 20-90.
On July 29, 2009, the CTA in Division denied petitioner’s Motion for Reconsideration.
Petitioner appealed to the CTA En Banc, which on March 1, 2010, affirmed the CTA in Division's decision and resolution, concurring that the assessments were barred by prescription due to defective waivers.
The petitioners’ ground before the Supreme Court questioned the CTA En Banc ruling on the basis of estoppel due to respondent’s partial payments on deficiency withholding taxes.

Whether the petitioner’s right to assess respondent for deficiency income tax, final income tax on FCDU, and EWT for taxable year 1998 was already barred by prescription under Section 203 of the National Internal Revenue Code (NIRC) of 1997, as amended, considering the alleged invalidity of the waivers of the statute of limitations for failure to comply with RMO No. 20-90 and jurisprudence.

Whether respondent is estopped from questioning the validity of the waivers of the statute of limitations by reason of partial payments made on WTC and FWT deficiency taxes.