Clarification on late fee for GSTR 9C!

As per section 44 of the CGST Act, 2017, every registered person shall furnish an annual return which may include a self-certified reconciliation statement, electronically, within such time and in such form and in such manner as may be prescribed. This means that filing of Form GSTR 9 and Form GSTR 9C i.e. Reconciliation statement, wherever applicable shall be together called Annual Return compliance. 

However, there was ambiguity about the applicability of late fees in cases where Form GSTR 9 and Form GSTR 9C were filed on different dates. This issue is now clarified vide Circular No. 246/03/2025-GST dated 30.01.2025.

Let’s dive deeper into it!

Circular No. 246/03/2025-GST dated 30.01.2025

‍

GOVERNMENT OF INDIA

MINISTRY OF FINANCE

DEPARTMENT OF REVENUE

CENTRAL BOARD OF INDIRECT TAXES AND CUSTOMS

GST POLICY WING

F. No. CBIC-20001/14/2024-GST

New Delhi: 30.01.2025

Circular No. 246/03/2025-GST

To,

All the Principal Chief Commissioners/ Chief Commissioners

All the Principal Directors General/ Directors General

Subject: Clarification on applicability of late fee for delay in furnishing of FORM GSTR-9C- reg.

1. Representations have been received seeking clarification regarding the levy of a late fee payable for delay in furnishing of reconciliation statement in FORM GSTR-9C. It has been requested to clarify whether a late fee under section 47 of the Central Goods and Services Tax Act, 2017 (hereinafter referred to as the "CGST Act") will be leviable where a reconciliation statement in FORM GSTR-9C is not furnished by the registered person along with the annual return in FORM GSTR-9 but is filed subsequently beyond the due date of furnishing of annual return.

2. In order to ensure uniformity in the implementation of the provisions of law across the field formations, the Board, in the exercise of its powers conferred by sub-section (1) of section 168 of the CGST Act, hereby clarifies the issues as below.

3. Prior to 01.08.2021, sub-section (2) of section 44 of the CGST Act provided that a registered person who is required to get his accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act shall furnish the annual return under sub-section (1) of the said section along with a copy of the audited annual accounts and a reconciliation statement. From 01.08.2021 onwards, with the omission of the requirement of getting accounts audited in accordance with the provisions of sub-section (5) of section 35 of the CGST Act, sub-section (1) of section 44 of CGST Act provides for furnishing of annual returns which may include a self-certified reconciliation statement, reconciling the value of supplies declared in the return furnished for the financial year, with the audited annual financial statement for every financial year electronically, within such time and in such form and in such manner as may be prescribed. Further, before 01.08.2021, sub-rule (3) of rule 80 of Central Goods and Services Tax Rules, 2017 (hereinafter referred to as the "CGST Rules") provided that accounts shall be audited as per sub-section (5) of section 35 of the CGST Act in case the aggregate turnover of a registered person exceeded two crore rupees in a financial year and such taxpayer shall furnish a copy of audited annual accounts and a reconciliation statement, duly certified, in FORM GSTR-9C. From 01.08.2021 onwards, sub-rule (3) of rule 80 of CGST Rules provides that taxpayers with aggregate turnover during a financial year exceeding five crore rupees shall furnish a self-certified reconciliation statement as specified under section 44 of the CGST Act in FORM GSTR-9C along with the annual return in FORM GSTR-9 on or before the thirty-first day of December following the end of such financial year.

3.1 Therefore, on a combined reading of section 44 of CGST Act with rule 80 of the CGST Rules, it can be concluded that both pre and post-amendment, the provisions mandated that registered persons required to furnish an annual return in FORM GSTR-9 for a financial year shall also furnish along with it, a duly certified or self-certified reconciliation statement in FORM GSTR-9C, which reconciles the value of supplies declared in FORM GSTR-9 furnished for the said financial year with the audited annual financial statement. It is also mentioned that a reconciliation statement in FORM GSTR-9C is required to be filed only if the aggregate turnover of the said registered person during a financial year exceeds the specified threshold limit.

3.2 Sub-section (2) of section 47 of the CGST Act provides for a levy of a late fee for failure to furnish the return under section 44 of the CGST Act by its due date, which is to be computed at the specified rate, for each day for which such failure continues, subject to a maximum amount. As per the discussions above, in cases where a reconciliation statement in FORM GSTR-9C is not required to be furnished, annual return under section 44 of CGST Act consists only of FORM GSTR-9 and in cases where a reconciliation statement in FORM GSTR-9C is required to be furnished, the annual return under section 44 of CGST Act consists of the return in FORM GSTR-9 along with a reconciliation statement in FORM GSTR-9C. Therefore, in cases where the reconciliation statement in FORM GSTR-9C is required to be furnished along with the annual return in FORM GSTR-9, the furnishing of the annual return under section 44 of the CGST Act, may not be said to be complete, unless both returns in FORM GSTR-9 and reconciliation statement in FORM GSTR-9C are furnished. If only a return in FORM GSTR-9 is furnished and a reconciliation statement in FORM GSTR-9C is required but not furnished, an annual return under section 44 of the CGST Act cannot be said to have been furnished.

3.3 In view of the above, it is clarified that the 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 GSTR- 9C 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 the 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 the 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,

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

b. The date of furnishing of FORM GSTR-9C, if FORM GSTR-9C is furnished after the furnishing of FORM GSTR-9.

4. 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 more than 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 GSTR- 9C is furnished on or before 31st March 2025. Accordingly, in cases where a 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.

5. It is requested that suitable trade notices be issued to publicize the contents of this Circular.

6. Difficulty, if any, in the implementation of this Circular may be brought to the notice of the Board.

Gaurav Singh

Commissioner (GST)

Key features

• As per section 44 of the CGST Act, 2017, annual returns shall be filed up to 31^st December of the next Financial Year as follows:

‍

• U/s 47(2) of the CGST Act,2017, any registered person who fails to furnish the return required under section 44 by the due date shall be liable to pay a late fee of one hundred rupees for every day during which such failure continues subject to a maximum of an amount calculated at a quarter percent. of his turnover in the State or Union territory.
• Now, the important question that arises is whether the late fee is leviable if GSTR 9 is filed within the due date, but GSTR 9C is not filed even though applicable or filed after the due date.
• This circular addresses the above query as follows:

‍

• This circular clearly states that filing of annual return u/s 44 means filing of Form GSTR 9 along with Form GSTR 9C wherever applicable. Therefore, filing of Form GSTR 9 without Form GSTR 9C in applicable cases will not be considered as sufficient compliance. Late fees will be calculated till the date of filing Form GSTR 9C if it is filed on a later date than filing of Form GSTR 9.

• It is to be noted that late fees will not be calculated on each form i.e. GSTR 9 and GSTR 9C separately. It will be levied on the combined filing of the two forms.

• For FY 2017-18 till FY 2022-23, the relaxation is provided vide notification No. 08/2025-Central Tax dated 23.01.2025. It is stated therein that in cases where a reconciliation statement in FORM GSTR-9C was required to be furnished along with the return in FORM GSTR-9, but was not furnished, and has been furnished subsequently on or before 31st March 2025, then late fees will be calculated till the date of filing GSTR 9 if filed late. Additional late fees for GSTR 9C filing will be waived. However, no refunds will be issued for late fees already paid.

Conclusion

The recent clarification provided by Circular No. 246/03/2025-GST has resolved the ambiguity regarding the applicability of late fees for GSTR-9C filing delays. It is now clear that the annual return under Section 44 of the CGST Act comprises both Form GSTR-9 and Form GSTR-9C (where applicable), and any delay in filing either will result in a late fee calculation until both forms are submitted. Additionally, the relief granted for financial years up to 2022-23 through Notification No. 08/2025 offers much-needed flexibility for businesses to comply without incurring excessive penalties. Taxpayers should ensure timely compliance with both filings to avoid unnecessary financial burdens and streamline their GST obligations effectively.