On January 30, 2025, the GST Policy Wing of the Central Board of Indirect Taxes and Customs (CBIC) issued to provide much-needed clarity on a common issue faced by many registered taxpayers — the applicability of late fees when FORM GSTR-9C (Reconciliation Statement) is filed after the due date, particularly when it’s not submitted alongside the FORM GSTR-9 (Annual Return).
The issue stemmed from queries regarding whether late fees under Section 47 of the CGST Act, 2017 apply if a taxpayer files GSTR-9 on time but delays the submission of GSTR-9C. Here’s a breakdown of the key clarifications provided in the circular:
Understanding the Legal Framework
Before 01.08.2021, the law required certain taxpayers (based on turnover) to get their accounts audited and submit GSTR-9C, duly certified by a chartered accountant, along with GSTR-9.
Post 01.08.2021, the audit requirement was removed, and a self-certified GSTR-9C was introduced. From that point on, taxpayers with a turnover exceeding ₹5 crore were required to furnish the reconciliation statement in GSTR-9C along with the annual return.
Key Clarifications from the Circular
Annual Return = GSTR-9 + GSTR-9C (if applicable): The CBIC clarified that the term “annual return” under Section 44 of the CGST Act includes both GSTR-9 and GSTR-9C wherever applicable. Hence, the annual return is not considered “furnished” unless both are submitted.
Late Fee Implications: If a taxpayer delays the filing of GSTR-9C (when it’s required), the late fee under Section 47(2) is applicable from the due date of the annual return until the date the complete return — both GSTR-9 and GSTR-9C — is furnished.
No Separate Late Fee for GSTR-9C: There will be no separate late fee for GSTR-9C alone. Instead, a combined late fee applies based on the delay in furnishing the full annual return.
Relief for Past Years (Up to FY 2022-23)
To ease compliance pressure, the circular also refers to Notification No. 08/2025-Central Tax (dated 23.01.2025). Under this:
For FYs up to 2022-23, additional late fees for delayed GSTR-9C filings are waived, provided that GSTR-9C is filed on or before March 31, 2025, and GSTR-9 had already been filed.
However, no refund will be issued for any late fees already paid for previous delays.
Conclusion
This circular brings welcome clarity and standardization to the treatment of delayed GSTR-9C filings. It highlights the importance of treating GSTR-9 and GSTR-9C as a composite compliance requirement for eligible taxpayers. Additionally, the waiver for late fees up to FY 2022-23 offers a relief window for those who missed deadlines in earlier years.
Taxpayers are encouraged to review their filings and make use of the waiver period ending March 31, 2025, while also aligning future filings to avoid late fee liabilities under Section 47.
For those impacted, now is the time to act — file pending GSTR-9C forms before the deadline and stay compliant.
