Late Fees and Interest on GST Returns Explained by Disytax

When a business doesn’t file a GST (Goods and Services Tax) return or pay tax liability on time, the department will charge late fees and interest. Hence, understanding these aspects is important for businesses. This article covers all about interest and late fees under GST.

Taxpayer Due Dates Under GST

The due dates for GST returns depend on the type of taxpayer and return forms.

 **For the taxpayers with aggregate turnover equal to or below Rs 5 crore, eligible and remain opted into the QRMP scheme, 22nd of month next to the quarter for taxpayers in category X states/UTs and 24th of month next to the quarter for taxpayers in category Y states/UTs 

Category X: Chhattisgarh, Madhya Pradesh, Gujarat, Maharashtra, Karnataka, Goa, Kerala, Tamil Nadu, Telangana or Andhra Pradesh or the Union territories of Daman and Diu and Dadra and Nagar Haveli, Puducherry, Andaman and Nicobar Islands and Lakshadweep.

Category Y: Himachal Pradesh, Punjab, Uttarakhand, Haryana, Rajasthan, Uttar Pradesh, Bihar, Sikkim, Arunachal Pradesh, Nagaland, Manipur, Mizoram, Tripura, Meghalaya, Assam, West Bengal, Jharkhand or Odisha or the Union Territories of Jammu and Kashmir, Ladakh, Chandigarh and New Delhi.

Please note: GST filings as per the CGST Act are subject to changes by CBIC notifications/orders.

Interest on Late Payment of GST

Interest is applicable on late payment of GST liability on the net tax liability after reducing the input tax credit claims. Interest charges apply when a taxpayer does not pay the GST amount by the respective due date. (You can find the list of GST due dates in the section above). 

 The interest has to be paid by every taxpayer who:

• Makes a delayed GST payment i.e. pays CGST, SGST or IGST after the due date.
• Claims excess input tax credit
• Reduces excess output tax liability

If GST is not paid within the due dates of filing return Interest at following rates has to be paid:

For example, a taxpayer fails to make a tax payment of Rs.10,000 for the month of January 2025, where the due date was 20th February 2025.

If they make the payment on 22nd March 2025, the interest for the delay period (30 days: from 21st February till 22nd March) will be calculated as follows:
Interest = (Outstanding Tax x Interest Rate x Number of Days) / 365
Interest = (10,000 x 18% x 30) / 365 = ₹147.95

GST Late Fees: Penalty for Delayed Filing (Section 47 of CGST Act)

Section 47 of CGST Act is the legal basis for levying late fees when a registered taxpayer fails to furnish the required GST returns by their respective due dates. The late fee is automatically calculated by the GST system once the due date is crossed.

As per the GST laws, late fee is an amount charged for delay in filing the GST returns. It is a penalty charged for missing the GST return filing due date. The department prescribed late fees charged for each day of delay from prescribed due dates as listed in the section above.

The late fee is also applicable for the delay in filing nil returns. For example, one has to pay a late fee even though there are no sales or purchases and no GST liability to declare in the GSTR-3B.

The late fee will depend upon the number of days of delay from the due date of respective return .

For example, GSTR-3B is filed on 23rd January 2025, 3 days after the prescribed due date i.e 20th January 2025. The late fees will be calculated for three days and it should be deposited in cash.

The GST portal charges a late fee on GST returns such as:

• GSTR-1 Statement of outward supplies (details of sales).
• GSTR-3B Monthly (or quarterly for QRMP scheme) summary return for reporting supplies and paying tax.
• GSTR-4 Annual return specifically for taxpayers registered under the Composition Scheme.
• GSTR-5 Every registered non-resident taxable person is required to furnish a return in GSTR-5 in GST Portal.
• GSTR-5A GST Return For Non-Resident OIDAR Service Providers
• GSTR-6 Monthly GST return that every Input Services Distributor must file for furnishing details of input service invoices on which credit has been received and needs to be distributed.
• GSTR-7 Monthly return required by persons deducting Tax Deducted at Source (TDS) under GST.
• GSTR-8 Monthly statement required by e-commerce operators collecting Tax Collected at Source (TCS) under GST.
• GSTR-9 Annual return for regular taxpayers.

Note: The late fee should be paid in cash and the taxpayer cannot use the Input Tax Credit (ITC) available in electronic credit ledger for payment of late fee.

Late Fees and Penalties Under GST

The following is the list of late fees and penalties under the GST law for delayed filing of GST returns beyond the due dates listed above.

Late Fee Computation for GSTR-3B and GSTR-1

• As per the GST Acts, for intrastate supplies, the late fee should be paid under both the CGST and SGST Act as follows:

• The Nil return filers must pay the below mentioned late fee:

For example, a taxpayer has filed GSTR-3B for February 2025 on 23rd March 2025, where the actual due date was 20th March 2025.

Amount of late fees to be paid would be Rs.150 (Rs. 50 per day for 3 days). The late fee would be Rs.75 under CGST and Rs.75 under SGST.

If the above return was a return with ‘Nil’ tax liability then late fees would be Rs. 60 (20 per day  3 days). The late fee would be Rs.30 under CGST and Rs.30 under SGST.

Late Fees for GST annual return (GSTR-9)

*CBIC issued notification no: 07/2023–Central Tax to reduce late fee for delayed GSTR-9 filing from FY 2022-23 onwards:

1. Reduced the late fee for GSTR-9 from FY 2022-23:
   1. Taxpayers whose Annual Aggregate Turnover (AATO) is up to Rs.5 cr shall pay Rs. 50 per day subject to a maximum of 0.04% of turnover in state or union territory.
   2. Taxpayers whose AATO is more than Rs.5 cr to 20 cr shall pay Rs 100 per day subject to a maximum of 0.04% of turnover in state or union territory.
2.  Also, taxpayers who file pending GSTR-9 for FYs 2017-18, 2018-19, 2019-20, 2020-21, and 2021-22 shall pay a maximum late fee of Rs 20,000. This reduced late fee applies only when you file pending GSTR-9 between 01st April 2023 to 30th June 2023.

Maximum Amount of Late Fees Under GST

Note that the maximum late fees have been rationalised from the month of June 2021 and quarter ending June 2021.

As per the 43rd GST Council meeting’s outcome, maximum late fee is reduced to the following amounts based on type of return and turnover slab, notified via the CGST notifications 19/2021, 20/2021,21/2021 dated 1st June 2021 for GSTR-3B and GSTR-1.

Further, according to CGST notification 22/2021 dated 1st June 2021, the late fee chargeable for GSTR-7 is reduced from Rs.200 to Rs.50 per day of delay, per act, per return.

List of Late Fee Notifications (Up to 2025):

This section includes notifications mentioned in your document:

GSTR-1

• June 2021 onwards (monthly) and quarter-ended June 2021 onwards (QRMP): Maximum late fee reduced, with specific caps for Nil filers (Rs. 500 per return) and others based on turnover slabs. (Notification 20/2021)
• Months March 2020 – June 2020 and Quarter ending 31st March 2020 and 30th June 2020: Waived off completely if filed before specified dates of July-August 2020. (Notification 53/2020)
• Months March 2020 – April 2020 and Quarter ending 31st March 2020: Waived off completely if filed before specified dates of June-July 2020. (Notification 33/2020)
• July 2017 – November 2019: Waived off completely if filed between 19th December 2019 to 10th January 2020. (Notification 74/2019)
• July 2019: Waived off completely for taxpayers in certain flood-affected districts and all districts of J&K. (Notification 41/2019)
• July 2017 – September 2018: Waived off completely. (Notification 75/2018)
• July 2017 onwards: Reduced Late fee. (Notification 4/2018)

GSTR-3B

• For June 2021 onwards (monthly) and quarter-ended June 2021 onwards (QRMP): Maximum late fee reduced, with specific caps for Nil filers (Rs. 500 per return) and others based on turnover slabs. (Notification 19/2021)
• From July 2017 to April 2021: Conditional waiver of late fee if filed between 1st June to 31st August 2021, with maximum late fee at Rs. 500 per act per return. (Notification 19/2021)
• For monthly filers: March and April 2021; For quarterly filers: Jan-Mar 2021: Conditional waiver of late fee (No late fee for 15 days delay for turnover > Rs. 5 crore; No late fee for 30 days delay for turnover <= Rs. 5 crore). (Notification 09/2021)
• For turnover > Rs 5 crore (May 2020 – July 2020); For turnover <= Rs 5 crore (February 2020 – July 2020): Maximum late fee capped at Rs. 500 per return filed after specified dates but before 30th September 2020 (Nil return no late fee). (Notification 57/2020)
• Various periods (February 2020 – July 2020, July 2017 – January 2020 pending): Conditional waivers and maximum fee caps if filed within specified dates in June-September 2020. (Notification 52/2020)
• February 2020 – April 2020: Waived off completely if filed before staggered specified dates of June-July 2020. (Notification 32/2020)
• October 2018 onwards: Reduced Late fee. (Notification 76/2018)
• July 2017 – September 2018: Reduced Late fee if filed beyond 31st March 2019; Waived off completely if filed between 22nd Dec 2018 to 31st March 2019. (Notification 76/2018)
• October 2017 only: Waived off completely for GSTR-3B submission made but not filed due to a technical glitch. (Notification 41/2018)
• October 2017 – April 2018 (for those who submitted TRAN-1 but couldn’t file GSTR-3B): Waived off completely if TRAN-1 filed by 10th May 2018 and GSTR-3B by 31st May 2018. (Notification 22/2018)
• October 2017 onwards: Reduced Late fee if date of filing was before 22nd December 2018. (Notification 64/2017)
• July 2017 – September 2017: Waived off completely if date of filing was before 22nd December 2018. (Notifications 28/2017 and 50/2017)

GSTR-4 (Annual)

• FY 2021-22 onwards: Maximum late fee restricted to Rs. 500 per return for nil filing and Rs. 2,000 for other than nil filing. (Notification 21/2021)

GSTR-5

• July 2017 onwards: Reduced Late fee. (Notification 5/2018)

GSTR-5A

• Returns for July 2017 onwards filed on or after 7th March 2018: Full Late fee applicable. (Notification 13/2018)
• July 2017 onwards: Reduced Late fee. (Notification 5/2018)

GSTR-6

• July 2019: Waived off completely for taxpayers in certain flood-affected districts and all districts of J&K. (Notification 41/2019)
• For any tax period prior to January 2018: Completely waived off. (Notification 41/2018)
• July 2017 onwards: Reduced Late fee (No late fees for Nil return). (Notification 7/2018)

Recent Notifications (2022-2025):

• Notification No. 07/2023-Central Tax (March 31, 2023): Implemented the 2023 GST amnesty scheme, offering concessional late fees for delayed filing of GSTR-4, GSTR-9, and GSTR-10 for past financial years. For GSTR-9 (FY 2017-18 to 2021-22), allowed filing with a concessional maximum late fee of Rs. 20,000 if filed between 1st April 2023 and 30th June 2023.
• Notification No. 08/2023-Central Tax (March 31, 2023): Allowed filing GSTR-10 (Final return) with a concessional maximum late fee of Rs. 1,000 if filed between 1st April 2023 and 30th June 2023.
• Notification No. 23/2024-Central Tax (October 8, 2024): Waived late fees for delayed filing of GSTR-7 from June 2021 onwards. The waiver applies to amounts exceeding ₹25 per day (capped at ₹1,000 total). Complete waiver for months where total TDS was Nil. This notification came into effect from November 1, 2024.
• Notification No. 08/2025-Central Tax (January 23, 2025): Waived late fees for delayed filing of the reconciliation statement in FORM GSTR-9C for Financial Years 2017-18 to 2022-23. This waiver is applicable if GSTR-9C is filed on or before March 31, 2025. It waives the late fee in excess of the amount payable up to the date of furnishing GSTR-9. However, no refund is available for late fees already paid for delayed GSTR-9C filing for these years. This notification provides relief to taxpayers who filed GSTR-9 but delayed filing GSTR-9C.
• Circular No. 246/03/2025-GST (Issued by CBIC): Clarified the applicability of late fees for delays in furnishing FORM GSTR-9C, particularly in relation to GSTR-9 filing. It reiterates that late fee applies for the delay in furnishing the complete annual return (GSTR-9 plus GSTR-9C, where applicable). It also references the waiver provided by Notification No. 08/2025-Central Tax for FYs up to 2022-23 if GSTR-9C is furnished by March 31, 2025.

This list should give you a good overview of the significant changes and waivers in GST late fees through early 2025.

How to Pay Late Fees on the GST portal?

The late fee applicable will be automatically calculated by the GST portal while submitting the GST returns. The current month/quarter late fee should be paid when filing the next month/quarter returns.

The late fee is paid in cash separately for CGST, and SGST in separate electronic cash ledgers. GST return cannot be filed without the payment of the Late fee.

Late fee for the month includes previous month’s late fee charged due to delay in filing of the return. Also, non-payment or late payment of GST attracts Interest.

Rules Applicable for GST Payment for Taxpayers

GST payment rules vary based on a few factors. Here are the main rules for regular taxpayers, composition scheme taxpayers, and casual taxable persons:
1.  Regular Taxpayers: Must file GSTR-1 and GSTR-3B. Filing must include payment of due tax to avoid interest and late fees.
2.  Composition Scheme Taxpayers: Taxpayers under the composition scheme file returns annually (GSTR-4) but must make quarterly payments via CMP-08. Late payments attract both interest and penalties.
3.  Casual Taxable Persons: Casual taxpayers, such as those temporarily engaged in business, need to register for GST and pay taxes in advance based on their estimated liability. Failing to pay on time incurs penalties similar to regular taxpayers.
 

Each category of taxpayers has its own rules in regard to return forms and deadlines, but the general advice is the same—meet the due dates to avoid extra charges. In addition, taxpayers must maintain proper documentation to support GST payments and input tax credit claimed.

Clear Tax Compliance with Disytax

• Accurate GST Return Filing: Helping businesses prepare and file GSTR-1, GSTR-3B, and other relevant returns correctly and on time, minimizing errors that could lead to late fees and interest.
• Input Tax Credit (ITC) Management: Assisting in matching purchase data with GSTR-2A/2B to ensure eligible ITC is claimed accurately and to identify discrepancies.
• E-way Bill Generation: Facilitating the correct and timely generation of E-way Bills for the movement of goods.
• Reconciliation: Helping reconcile sales and purchase data with GST returns and other relevant records.
• Staying Updated: Providing updates on changes in GST laws, rules, and notifications to ensure ongoing compliance.
• Avoiding Penalties: By automating calculations, providing alerts for due dates, and reducing errors, such a service helps businesses avoid penalties like late fees and interest.