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Can a penalty of Rs. 50,000 u/s 125 of the CGST & SGST Act, 2017 be imposed directly in case of delayed filing of Form GSTR-9C ?

Form GSTR-9C i.e. Reconciliation Statement forms part of Annual Return specified under Section 44 of the CGST Act, 2017. Those registered persons whose Aggregate Turnover exceeds Rs. 5 Crores are required to file it before 31st December each year along with GSTR-9.

As per Section 47(2) of the CGST Act, 2017, in case of delayed filing of return specified u/s 44, a Late Fees of Rs.100 per day shall be applicable subject to maximum of 0.25% of turnover in a state. Similar provision is there in respective State GST Acts which makes a total late fees of Rs. 200 per day for delayed period.

Currently portal computes late fees till date of GSTR-9 and not for GSTR-9C which is filed beyond the date of filing GSTR-9. The only option which the registered person has for depositing late fees of GSTR-9C filed beyond GSTR-9 is to declare the same in  Part V of GSTR-9C and pay the same via DRC-03.

Let us understand with the help of an example –

Last date for filing of Annual Return u/s 44 for F.Y. 2021-22 was 31st December 2022.

GSTR-9 filed on 02.01.2023 – Late Fees of Rs.400 shall apply. (Rs.200 for 2 days)

GSTR-9C filed on 05.01.2023 – Late Fees of Rs.600 shall be applied. (Rs.200 for 5 days less Rs.200 for 2 days already paid)

Now let us talk about the provisions for delayed filing of Form GSTR-9C:

Firstly, in case of failure to furnish the return specified under section 44 within due date, a notice shall be issued u/s 46 requiring the registered person to furnish the same within 15 days. The Notice u/s 46 shall be issued in Form GSTR-3A under Rule 68 of the CGST Rules, 2017.

Hence, additional 15 days shall be provided to the registered person to comply with the provisions of Section 44 and to file the Reconciliation Statement.

Secondly, as per Section 126(1), No penalty can be imposed for ‘minor breach of tax regulations’ or ‘procedural requirements’ or ‘any omission which is easily rectifiable’

Thirdly, if late fee is already charged for delayed filing of GSTR-9C, then penalty shall not be imposed for same delay again as per Principles of Natural Justice.

Hence, it can be concluded that no penalty can be levied directly u/s 125 of the CGST Act, 2017 for delay in filing of Form GSTR-9C.


DISCLAIMER : The information provided by the author in the article is for general information purpose only. We make no representation or warranty of any kind, express or implied, regarding the accuracy, adequacy, validity, reliability or completeness of any information in the article.

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  1. surbhi hansrajani says:

    Respected sir, my question is our firm not undergone gst audit from last four years due to negligience of CA. on 31st dec 22- 1st-jan 2023 we completed all gst audit with so much burden of penalties.
    can we request for refund??

  2. Raj says:

    Dear sir i received a notice for non filing of GSTR- 9 and 9C for the last four years, The penalty and late fees are shown in the notice are very high, This much of penalty and late fee we not able to pay, Kindly guide how to reduce the penalty and late fee. Thank you sir

  3. opjain02 says:

    Refer my article in magazine dated 9.7.2022 : (2022) 38 J.K.Jain’s GST & VR, page R-11 to R-12 concluding that for delayed submission of Reconciliation Statement GSTR-9C, neither the Late Fee is payable nor a penalty u/s 125, is payable.
    CA Om Prakash Jain s/o J.K.Jain, Jaipur
    Tel 9414300730/9462749040

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May 2024