How Late Fees are Calculated for GSTR-9C for FY 2024-25: Complete Compliance Guide
Three important dates are taken into account by the portal for calculating the applicable late fee: the annual return's statutory due date, the GSTR-9 filing date, and the GSTR-9C filing date.
The levy and computation of late fees for delayed filing of GSTR-9C had an uncertainty in the minds of taxpayers and professionals, especially on whether the delay should be linked only to GSTR-9C or to the annual return as a whole. This issue has been conclusively clarified by the CBIC through Circular No. 246/03/2025-GST dated 30 January 2025. As per the Circular, late fee is levied...
The levy and computation of late fees for delayed filing of GSTR-9C had an uncertainty in the minds of taxpayers and professionals, especially on whether the delay should be linked only to GSTR-9C or to the annual return as a whole.
This issue has been conclusively clarified by the CBIC through Circular No. 246/03/2025-GST dated 30 January 2025.
As per the Circular, late fee is levied under Section 47(2) of the CGST Act for delay in furnishing the “complete annual return” prescribed under Section 44, and this complete annual return consists of both FORM GSTR-9 and FORM GSTR-9C (where applicable). Therefore, delay in filing either of these forms has a direct bearing on late fee liability.
Statutory Basis: Sections 44 and 47(2) of the CGST Act- Explained Simply
Under the GST Act, Section 44 of the CGST Act lays down the requirement for filing annual returns. It mandates that eligible registered taxpayers must file FORM GSTR-9, which is the annual summary of all GST returns filed during the year.
Further, for taxpayers to whom audit provisions apply, FORM GSTR-9C which contains reconciliation of turnover, tax paid, and ITC as per books with GST returns along with certification is also required to be furnished. In effect, the annual return obligation is not complete merely by filing GSTR-9 where GSTR-9C is applicable.
Section 47(2) of the CGST Act deals with the consequences of delay. It clearly states that if a registered person fails to furnish the return required under Section 44 by the due date, a late fee is payable for every day of delay, subject to the maximum limit prescribed under the Act.
The CBIC, through its recent Circular, has clarified an important point of interpretation: the term “return under Section 44” does not mean only GSTR-9, but includes both GSTR-9 and GSTR-9C together wherever applicable.
Therefore, if GSTR-9 is filed on time but GSTR-9C is delayed, the annual return is considered incomplete, and late fee under Section 47(2) continues to apply until GSTR-9C is also filed. This clarification removes ambiguity and confirms that timely filing of both forms is important to avoid late fees.
Structural Change in the Form: Insertion of Table 17 in GSTR-9C
The GST 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. The purpose of this table is to capture 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.
Late Fee Computation Principles
The Circular introduced a clear, integrated, and sequential approach to the computation of late fees for annual returns under GST. In the first stage, the levy of late fee is anchored to the due date of the annual return (GSTR-9).
However, compliance is treated as complete only when the entire annual return obligation under Section 44 is fulfilled. Accordingly, where GSTR-9C is applicable, the late fee does not stop merely upon filing GSTR-9 but continues to accrue until GSTR-9C is also furnished.
Put simply, filing GSTR-9 alone does not conclude annual return compliance in cases where GSTR-9C is required. The accrual of late fee under Section 47(2) ceases only when both GSTR-9 and GSTR-9C are filed, ensuring that the annual return is complete in all respects.
Period for which Late Fee Is Leviable
According the GSTN clarification, the following are the period who which the late fee leviable:
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.
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.
System-Based Auto-Calculation of Late Fees
The Circular's main clarification is that late fees for both GSTR-9 and GSTR-9C are fully system-driven and automatically computed by the GST portal, removing the requirement for taxpayers or experts to perform the computation by hand.
Three important dates are taken into account by the portal for calculating the applicable late fee: the annual return's statutory due date, the GSTR-9 filing date, and the GSTR-9C filing date.
In cases where the GSTR-9 is filed after the deadline, the system first calculates and assesses a late charge for the duration of the delay up to the GSTR-9 filing. The portal then automatically carries forward the remaining delay period if GSTR-9C is filed later. This is shown in Table 17 of GSTR-9C, which records the late charge payable and paid under Section 47(2).
This automated mechanism ensures accuracy, prevents duplication of late fees for the same period, and provides a clear audit trail of how the total late fee has been apportioned between GSTR-9 and GSTR-9C filings.
