GSTR 9/ GSTR 9C: No Due Date Extension, Read the Circular on How Late Fee Applies with CBIC Clarification
Since there has been no notice of an extension, late fees under Section 47 will still be applicable for return filing that is delayed.
The Government has not extended the due date for filing GSTR-9 (Annual Return) and GSTR-9C (Reconciliation Statement), despite repeated industry representations. So what next? You can file the returns but with an additional fee as per the statute. Since there has been no notice of an extension, late fees under Section 47 will still be applicable for return filing that is delayed....
The Government has not extended the due date for filing GSTR-9 (Annual Return) and GSTR-9C (Reconciliation Statement), despite repeated industry representations. So what next? You can file the returns but with an additional fee as per the statute.
Since there has been no notice of an extension, late fees under Section 47 will still be applicable for return filing that is delayed.
If you fail to file the returns could result in departmental scrutiny, notices, and audit exposure, especially if there are discrepancies between GSTR-1, GSTR-3B, and books of accounts.
How the late fees are calculated in GSTR 9C for FY 2024-25
The late fee shall be leviable for the period starting from the due date of furnishing the annual return till the date of filing of GSTR 9 for annual return. And, the late fee for GSTR 9C will be calculated from date of filing of GSTR 9 or due date of filing of Annual return, whichever is later till the filling of GSTR-9C. These late fees will be auto calculated by the system based on the date filing of GSTR 9 and 9C.
Making it more clarified with an example. GSTR 9 was filed on December 25, 2025 (due on December 31, 2025), and GSTR 9C filed on January 7, 2026. Since GSTR 9 was submitted by the deadline, there are no late costs. However, GSTR 9C automatically populates late fees for seven days (delay in providing of GSTR 9C).
Another situation is that GSTR 9 is furnished on 5th January 2026 and GSTR 9C is furnished on 7th January 2026. Then total late fees leviable is for 7 days which will be auto populated by the system as For 5 days at the time of filing GSTR 9 and for balance 2 days will be populated in GSTR 9C at the time of filing GSTR 9C.
Additionally, the ministry has made changes to the GST portal regarding the late fee. The portal has added a new Table 17 called "Late Fee Payable and Paid" beneath Part V of GSTR-9C in order to carry out this clarification by the board. This is to enter the late fee payable under Section 47(2), and reflect the portion of late fee already discharged (if any) at the time of filing GSTR-9.
CBIC Circular
The CBIC, through circular No. 246/03/2025-GST has clarified that late fee under Section 47 of the CGST Act is leviable for delay in furnishing a complete annual return, meaning both GSTR-9 and GSTR-9C, wherever GSTR-9C is mandatory.
Merely filing GSTR-9 without GSTR-9C does not amount to filing of the annual return, and late fee will continue to accrue till the date GSTR-9C is furnished, states the circular.
However, for financial years up to FY 2022-23, the Government has granted a one-time relief: if GSTR-9C is filed on or before 31 March 2025, no additional late fee will be payable beyond what was due up to the date of filing GSTR-9, though no refund of late fee already paid will be allowed.
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