An overview of GST Circular No. 246/03/2025 on Late Fee for Delay in Filing FORM GSTR-9C
1. Late Fee Applicability for FORM GSTR-9C Filing Delay
Queries were raised regarding whether late fees under Section 47 of the CGST Act apply when FORM GSTR-9C (reconciliation statement) is filed after the due date of the annual return (FORM GSTR-9).
2. Regulatory Background:
Before 01.08.2021: Registered persons with turnover exceeding ₹2 crore were required to get their accounts audited and submit a certified reconciliation statement (FORM GSTR-9C) along with their annual return (FORM GSTR-9).
After 01.08.2021: The mandatory audit requirement was removed. Now, taxpayers with turnover exceeding ₹5 Crore must submit a self-certified reconciliation statement (FORM GSTR-9C) along with FORM GSTR-9.
3. Clarification on Late Fees:
If FORM GSTR-9C is required but not filed along with FORM GSTR-9, the annual return is considered incomplete.
Late fees under Section 47(2) of the CGST Act will apply from the due date of the annual return until the complete return (both FORM GSTR-9 and FORM GSTR-9C) is submitted.
No separate late fee for delays in filing FORM GSTR-9 and FORM GSTR-9C; it will be calculated based on the complete annual return submission.
4. Waiver of Late Fee for Past Years (Upto FY 2022-23):
As per Notification No. 08/2025-Central Tax (dated 23.01.2025), excess late fees for delays in filing FORM GSTR-9C for financial years up to FY 2022-23 have been waived, provided it is filed on or before 31st March 2025.
However, no refund will be given for late fees already paid for past delays.
The copy of the circular is as under: