FAQ On Waiver of Late Fees on GSTR 9 And/or GSTR9C

The CBIC issued Notification No. 08/2025 – CENTRAL TAX on January 23, 2025, implementing a decision from the 55th GST Council meeting regarding the waiver of late fees on GSTR-9 and GSTR-9C filings. This waiver applies to filings for FY 2017-18 through FY 2022-23, provided GSTR-9C is filed by March 31, 2025. Late fees already paid will not be refunded. The notification details updates to the filing process and penalties under Section 44 and Rule 80 of the CGST Act. It clarifies that, until July 31, 2021, audited accounts and a reconciliation statement were mandatory. However, from August 1, 2021, the requirement shifted to a self-certified reconciliation statement.

The FAQs address various scenarios for taxpayers regarding late fee applicability. Key clarifications include:

1. GSTR-9 filings are incomplete without GSTR-9C where applicable.

2. Filing GSTR-9C after the March 31, 2025 deadline will attract late fees.

3. For FY 2017-18 to 2022-23, late fees for delayed GSTR-9 filings are waived if GSTR-9C is filed by March 31, 2025.

4. From FY 2023-24, late fees for GSTR-9 filings will also account for delays in GSTR-9C submissions, wherever applicable.

Taxpayers are encouraged to use this one-time opportunity to file pending GSTR-9C without incurring additional penalties.

I would like to reproduce the relevant part of the Notification here

> In exercise of the powers conferred by section 128 of the Central Goods and Services Tax Act, 2017 (12 of 2017) (hereinafter referred to as the said Act), the Central Government, on the recommendations of the Council,

> hereby waives the amount of late fee referred to in section 47 of the said Act

> in respect of the return to be furnished under section 44 of the said Act,

> for the financial years 2017-18 or 2018-19 or 2019-20 or 2020-21 or 2021-22 or 2022-23,

> which is in excess of the late fee payable under section 47 of the said Act upto the date of furnishing of FORM GSTR-9 for the said financial year,

> for the class of registered persons,

> who were required to furnish reconciliation statement in FORM GSTR-9C along with the annual return in FORM GSTR-9 for the said financial year

> but failed to furnish the same along with the said return in FORM GSTR-9,

> and furnish the said statement in FORM GSTR-9C, subsequently on or before the 31* March, 2025:

Provided that no refund of late fee already paid in respect of delayed furnishing of FORM GSTR-9C for the said financial years shall be available.

Now let us understand the evolution of Annual Returns over the years

Section 44. Annual return.

(1) Every registered person,

> other than an Input Service Distributor, a person paying tax under section 51 or section 52, a casual taxable person and a non-resident taxable person,

> shall furnish an annual return

> for every financial year electronically in such form and manner as may be prescribed

> on or before the thirty-first day of December following the end of such financial year.

Provided that the Commissioner may, on the recommendations of the Council and for reasons to be recorded in writing, by notification, extend the time limit for furnishing the annual return for such class of registered persons as may be specified therein:

Provided further that any extension of time limit notified by the Commissioner of State tax or the Commissioner of Union territory tax shall be deemed to be notified by the Commissioner.

(2) Every registered person

> who is required to get his accounts audited in accordance with the provisions of sub-section (5) of section 35

> shall furnish, electronically, the annual return under sub-section (1)

> along with a copy of the audited annual accounts and a reconciliation statement,

> reconciling the value of supplies declared in the return furnished for the financial year with the audited annual financial statement, and such other particulars as may be prescribed.

35(5) Every registered person  ( 1.7.17 to 31.7.21)

> whose turnover during a financial year exceeds the prescribed limit

> shall get his accounts audited by a chartered accountant or a cost accountant and

> shall submit a copy of the audited annual accounts, the reconciliation statement under sub-section (2) of section 44 and such other documents in such form and manner as may be prescribed.

Wef 01.08.2021 vide Notification no.29/2021- central tax dated 30.07.2021 Section 44 was substituted as follows:

Section 44. Annual return. –

[(1)] Every registered person,

> other than an Input Service Distributor, a person paying tax under section 51 or section 52, a casual taxable person and a non-resident taxable person

> shall furnish an annual return

> 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:

Provided that the Commissioner may, on the recommendations of the Council, by notification, exempt any class of registered persons from filing annual return under this section:

Rule 80. Annual return.- ( 1.7.17 to 31.7.21)

(1) Every registered person, other than an Input Service Distributor, a person paying tax under section 51 or section 52, a casual taxable person and a non-resident taxable person, shall furnish an annual return as specified under sub-section (1) of section 44 electronically in FORM GSTR-9 through the common portal either directly or through a Facilitation Centre notified by the Commissioner:

Provided that a person paying tax under section 10 shall furnish the annual return in FORM GSTR-9A.

(2) xxxxxxxxxxxxxxx .

For FY 2017-18

(3) Every registered person [other than those referred to in the proviso to sub-section(5) of section 35, ] whose aggregate turn over during a financial year exceeds two crore rupees shall get his accounts audited as specified under sub-section (5) of section 35 and he shall furnish a copy of audited annual accounts and a reconciliation statement, duly certified, in FORM GSTR-9C, electronically through the common portal either directly or through a Facilitation Centre notified by the Commissioner.

For FY 2018-19 and 2019-20

[ Provided that for the financial year 2018-2019 and 2019-2020, every registered person whose aggregate turnover exceeds five crore rupees shall get his accounts audited as specified under sub-section (5) of section 35 and he shall furnish a copy of audited annual accounts and a reconciliation statement, duly certified, in FORM GSTR-9C for the said financial year, electronically through the common portal either directly or through a Facilitation Centre notified by the Commissioner.

RULE 80 ( WEF 1.8.21)

(1) Every registered person, other than those referred to in the second proviso to section 44, an Input Service Distributor, a person paying tax under section 51 or section 52, a casual taxable person and anon-resident taxable person, shall furnish an annual return for every financial year as specified under section 44 electronically in FORM GSTR-9 on or before the thirty-first day of December following the end of such financial year through the common portal either directly or through a Facilitation Centre notified by the Commissioner:

Provided that a person paying tax under section 10 shall furnish the annual return in FORM GSTR-9A .

²[(1A) Notwithstanding anything contained in sub-rule (1), for the financial year 2020-2021 the said annual return shall be furnished on or before the twenty-eighth day of February, 2022.

(2) Every electronic commerce operator required to collect tax at source under section 52 shall furnish annual statement referred to in sub-section (5) of the said section in FORM GSTR -9B .

(3) Every registered person,

√ other than those referred to in the second proviso to section 44, an Input Service Distributor, a person paying tax under section 51 or section 52, a casual taxable person and a non-resident taxable person,

√ whose aggregate turnover during a financial year exceeds five crore rupees,

√ shall also furnish a self-certified reconciliation statement as specified under section 44 in FORM GSTR-9C along with the annual return referred to in sub-rule (1), on or before the thirty-first day of December following the end of such financial year, electronically through the common portal either directly or through a Facilitation Centre notified by the Commissioner.]

²[(3A) Notwithstanding anything contained in sub-rule (3), for the financial year 2020-2021 the said self-certified reconciliation statement shall be furnished along with the said annual return on or before the twenty-eighth day of February, 2022.]

Analysis

1. Till 31.7.21 there was a requirement of getting the books audited u/s 35(5) and filing of the reconciliation statement with the audited accounts was mandated as per Section 44 (2)

2. However wef 1.8.21 the requirement of getting the books audited u/s 35(5) has been done away with and a self certified reconciliation statement was to be included.

3. Wef 1.8.21 as per the substituted Rule 80(3) self certified reconciliation statement has to be furnished along with the reconciliation statement.

Now we would like to address some of the FAQS

Q1: Whether GSTR9 includes GSTR 9C?

Ans. Going by the above provisions Gstr 9 includes GSTR9C ( where notified ) as per Section 44(2) of the CGST Act, 2017 till 31.7.21 and Section 44(1) wef 1.8.21 read with Rule 80 as amended.

Q2: I have already filed the GSTR9 for 21-22 on 31^st December but as there was confusion regarding applicability of GSTR 9C, If I don’t file it at all. Are there are any consequences now?

Ans. If a RTP files only GSTR9 where 9C is also applicable, filing of GSTR9 is not complete till 9C is filed as Section 44 read with Rule 80 mandates filing of both wherever GSTR9C is applicable. Therefore if the same is not filed within 31.3.25 late fees of GSTR9 will get extended from the date of filing of GSTR9 to the actual filing of GSTR9C after 31.3.25.

Q3: So in the above scenario if I file the GSTR9C for 21 -22 on 8^th August 25, then will I have to pay late fees?

Ans. As the tax payer has filed GSTR9C after 31^st 31^st March 25, then late fees from 31^st December 22 ( date of filing of GSTR9) to 8^th August 25 will be applicable for delay in filing of GSTR 9 for 21-22 as the filing of GSTR9 within due will not be considered to be complete. Hence late fee as per 47 will be applicable till the date of filing of 9C even if 9 is filed within due date as the tax payer has not filed the GSTR9C within 31^st March 25. Therefore if all such GSTR9Cs are filed within 31^st March 25, no further late fees will be payable.

Q4: RPL had filed its GSTR 9 for 22-23 on 30^th December 23 but filed its GSTR9C only 29^th November 24. Will he be liable to pay any late fees U/s 47?

Ans. Reply : For FY 17 18 to 22 23, where GSTR 9 is filed within due no late fee will be applicable even if  GSTR9C is filed after the due date. Here since the GSTR 9C is already filed even though belatedly no further late fees is payable for delay in filing of GSTR9 ( as it is considered that GSTR9C is a part of GSTR9 only)

Q5: Hasi Private Limited filed its GSTR9 for 2019-20 on 9^th January 20 and GSTR 9C on 12^th March 20. Will it have to pay late fee for both the delays – 9 days for GSTR9 and 71 days for GSTR9C

Ans. Reply : For FY 17 18 to 22 23 where both GSTR 9 and 9C are filed after due date but within 31^st March 25,  late fees will be applicable only for GSTR 9  and that too till the date of filing of GSTR9. There is no separate late fee for delay in filing of GSTR9C only the period of delay is to be computed till filing of GSTR9C. However for the period FY 17-18 to 22-23 late fee for the additional period of delay between filing of GSTR9 and GSTR9C is waived.

Q6: I have filed the GSTR9 with or without late fees but have not filed the GSTR9C for any financial year during FY 17-18 to 22-23. Now if I file the GSTR9C within 31^st March 25, will I need to pay any late fees. 

Ans. REPLY  In case GSTR 9 is already filed with or without late fees but GSTR9C is not filed then one time opportunity of filling for 17 18 to 22 23 is given till 31.3.25 without any late fees for filing GSTR9C without any late fees.

Q7: For FY 23-24 onwards how will the late fee be computed ?

Ans. Reply :  From FY 23-24 onwards late fees for GSTR9 will be considered till date of filing of GSTR9C wherever GSTR9C is applicable. However only late fees for delay in filing of GSTR 9 will be payable as it will be considered that GSTR9 is filed only the self certified reconciliation statement is also filed by the taxpayer along with GSTR9 wherever it is applicable.

If i have missed any FAQS kindly share the question on mail please. So will add here for the benefit of all.