CBIC issues new clarifications about how waiver of late fees to file pending GSTR-9C by on or before March 31, 2025 will be calculated

Waiver of late fee for filing pending GSTR-9C by March 31, 2025: CBIC clarifies who is eligible and how to calculate

Goods and Services Tax (GST) registered taxpayers who failed to file GSTR-9C, which is a reconciliation statement filed along with GSTR-9 annual return, can now file GSTR-9C on or before March 31, 2025, to get a complete waiver of all late fees. This late fee is up to Rs 200 per day for a maximum of 0.5% of turnover. This will now be waived off provided taxpayers file their pending GSTR-9C before the date specified above.

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According to CBIC, multiple representations have been received by taxpayers about how exactly the waiver of late fees be calculated since GSTR-9C cannot be filed independently without first filing the GSTR-9 annual return.

CBIC on January 30, 2025, issued a circular to give clarity about how the waiver will be calculated and which taxpayers are going to be eligible for this waiver of late fees.

Clarifications given by CBIC about waiver of late fees for filing pending GSTR-9C return on or before March 31, 2025

The latest original deadline to file both GSTR-9 and GSTR-9C was December 31, 2023, for eligible taxpayers to receive waiver for FY 2022-23. However, this waiver is applicable to the previous 5 more years. The waiver of late fees for GSTR-9C relates to FY 2017-18, FY 2018-19, FY 2019-20, FY 2020-21, FY 2021-22 or FY 2022-23.

What is the condition to avail this late fee waiver on pending GSTR-9C?

Not all taxpayers are eligible to get this waiver as it comes with certain conditions.

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Chartered Accountant Hunny Munjal says, “The clarification number 2 means if a GST registered taxpayer failed to file GSTR-9 and GSTR-9C both on or before the deadline then the late fees will be limited to GSTR-9 and not GSTR-9C. For example, a taxpayer filed GSTR-9 late by 2 months and GSTR-9C late by 1 year. So late fees for 2 months need to be paid, the late fees for 1 year will be waived off provided this GSTR-9C is filed on or before March 31, 2025.”

Waiver of late fees is limited to the period of non-filing of GSTR-9

It is further mentioned that vide notification No. 08/2025-Central Tax dated 23.01.2025, the late fee in respect of delayed filing of complete annual return for any financial year up to FY 2022-23 has been waived, which is in excess of the late fee payable under sub-section (2) of section 47 of CGST Act up to the date of furnishing of return in FORM GSTR-9 for the said financial year, if the reconciliation statement in FORM GSTR9C is furnished on or before 31st March 2025.

Accordingly, in cases where reconciliation statement in FORM GSTR-9C was required to be furnished along with the return in FORM GSTR-9, but was not furnished so for any financial years up to FY 2022-23, and has been furnished subsequently on or before 31st March, 2025, then no additional late fee shall be payable for delayed furnishing of FORM GSTR-9C which is in excess of the late fee payable under section 47 up to the date of furnishing FORM GSTR-9 for the said financial year.

Further, no refund shall be admissible in respect of any amount of late fee already paid in respect of delayed furnishing of FORM GSTR-9C for the said financial years.

No separate late fees for filing GSTR-9C other than what levied on GSTR-9

It is clarified that late fee under sub-section (2) of section 47 of the CGST Act, is leviable for the delay in furnishing of complete annual return under section 44 of the CGST Act, i.e. both FORM GSTR-9 and FORM GSTR-9C (where FORM GSTR9C is also required to be furnished) and the late fee shall be payable for the period from the due date of furnishing of the said annual return up to the date of furnishing of the complete annual return i.e. Form GSTR-9 and Form GSTR-9C.

It is also to be noted that late fee is not separately leviable for delayed furnishing of FORM GSTR-9 and delayed furnishing of FORM GSTR-9C but has to be calculated for the period from the due date of furnishing of annual return under section 44 of the CGST Act till the date of furnishing of complete annual return i.e

I. In cases where FORM GSTR-9C is not required to be furnished, the date of furnishing of FORM GSTR-9;
ii. In cases where FORM GSTR-9C is required to be furnished along with FORM GSTR-9:

The date of furnishing of FORM GSTR-9, if FORM GSTR-9C is furnished along with FORM GSTR-9; or
The date of furnishing of FORM GSTR-9C, if FORM GSTR-9C is furnished subsequent to furnishing of FORM GSTR-9

This story originally appeared on: India Times - Author:Faqs of Insurances