Bombay CA Society Seeks 3-Month Extension for GSTR-9 & 9C Due Date, Raises Compliance Complexity [Read Representation Copy]

The Bombay Chartered Accountants’ Society ( BCAS ) has requested the Union Finance Ministry, the Central Board of Indirect Taxes and Customs ( CBIC ), and the GST Council to grant a minimum three-month extension for filing GSTR-9 (Annual Return) and GSTR-9C (Reconciliation Statement) for FY 2024-25, citing compliance complexity arising from recent amendments .

The yearly GST compliance structure has gone through frequent and profound changes, especially through Notifications 12/2024-CT and 13/2025-CT, which radically altered existing requirements for reporting in GSTR-9 and GSTR-9C, says BCAS's representation dated December 11, 2025.

The Society claims that these changes amount to a large change in policy, requiring taxpayers and experts to rethink reconciliation procedures that were regularly used for a number of years.

BCAS pointed out that the granularity introduced in Input Tax Credit (ITC) reporting has increased the effort required to prepare annual returns. New tables and mandatory break-ups now require taxpayers to segregate ITC of prior years availed in the current year, track reversals and re-availments under Rules 37 and 37A, and report import-related credits separately. These disclosures demand retrospective data tracking, which many taxpayers’ systems were not originally designed to capture.

The Society also identified major problems based on revisions to auto-population logic, especially in Table 8A, where the data population's foundation has frequently changed between GSTR-2A, GSTR-2B, document year, and return period. This has led to year-specific reconciliations for every GSTIN for FY 2024–2025 and, at times, technical issues where the final filed return differs from the draft annual return data, raising the possibility of discrepancies and departmental scrutiny.

Additionally, BCAS pointed out that starting in FY 2024–2025, the previous connection between Net ITC as per GSTR-3B and GSTR-9 has been broken. Existing reconciliation workbooks must be completely redesigned since taxpayers have to conform to a new reconciliation formula.

Further, this has resulted in discrepancies between books of accounts and GST returns due to inconsistent auto-populated data in GSTR-9C, especially when prior-year ITC is removed.

Regarding GSTR-9C, the Society also observed that reconciliation with audited financial accounts has become much more difficult due to the removal of previous reporting relaxations. The required table-wise reporting of cross-year ITC and turnover adjustments (Tables 12B and 12C) now requires a thorough mapping between GST returns and accrual-based financial statements, which takes more time and expertise.

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Additionally, BCAS reminded that the compilation of GSTR-9C depends entirely on audited financial accounts, which results in a vastly limited schedule for finishing yearly GST filings because tax audit deadlines have been extended until mid-November. Because annual returns must be filed separately for each registration, this burden is further increased for firms with multiple GST registrations across states.

As a result, BCAS requested for an ample extension of at least three months for GSTR-9 and GSTR-9C for all taxpayers, claiming that this relaxation will promote proper reporting, reduce conflicts, and benefit both compliant taxpayers and revenue authorities.

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