Stox N Tax

GST Late Fee in September 2025: Update

Table of Contents

  1. Introduction
  2. What Changed in September 2025?
  3. GST Return Due Dates to Remember
  4. Penalties and Late Fees Applicable
  5. How the ₹10,000 Fine Works Under Rule 59
  6. Example of Late Fee Calculation
  7. How to Pay GST Late Fees Online
  8. Key Mistakes Businesses Should Avoid
  9. FAQs
  10. Conclusion

1. Introduction

Timely filing of GST returns is one of the most important compliance requirements for businesses in India. Many small businesses delay filing due to cash flow issues, lack of accounting support, or simple oversight. However, in September 2025, the penalties for delayed filing have become more stringent.

The government amended Rule 59 of the CGST Rules, making businesses liable for a fine of up to ₹10,000 per return in addition to the standard late fees. This article explains what this change means, how penalties are calculated, and what businesses should do to stay compliant.

2. What Changed in September 2025?

Earlier, late fees were restricted to fixed amounts per day of delay. But now, as per the amendment to Rule 59 effective September 2025, businesses face an additional fine of ₹10,000 for non-filing or incorrect filing of GSTR-1.

This has been introduced to curb the mismatch between GSTR-1 and GSTR-3B, which affects tax credit claims of buyers.

3. GST Return Due Dates to Remember

  • GSTR-1 (Outward supplies): 11th of the next month
  • GSTR-3B (Summary return & tax payment): 20th of the next month (monthly filers)
  • Quarterly filers (QRMP Scheme): 13th of the month after the quarter ends

Missing these deadlines now comes with a heavier cost than before.

4. Penalties and Late Fees Applicable

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

  • ₹50 per day of delay (₹25 CGST + ₹25 SGST)
  • ₹20 per day for nil returns (₹10 CGST + ₹10 SGST)
  • Maximum capped at ₹5,000

New Fine Under Rule 59 (September 2025):

  • ₹10,000 per return if non-filing or discrepancies exist.

This is over and above late fees, making it a serious compliance risk.

5. How the ₹10,000 Fine Works Under Rule 59

If a business fails to file GSTR-1 on time, the department can levy:

  1. Standard late fee (per day of delay).
  2. A one-time fine of ₹10,000 for default under Rule 59.

This fine applies especially if the non-filing leads to mismatch with GSTR-3B or ineligibility of Input Tax Credit (ITC) for buyers.

6. Example of Late Fee Calculation

Suppose a small business with monthly filing missed filing GSTR-1 for August 2025 (due on 11th September).

  • Delayed filing: 15 days
  • Late fee = ₹50 × 15 = ₹750
  • Fine under Rule 59 = ₹10,000
  • Total = ₹10,750

For a small business, such costs can significantly affect cash flow.

7. How to Pay GST Late Fees Online

  1. Visit the GST Portal.
  2. Login with your GSTIN and password.
  3. Go to Returns Dashboard → Select Period.
  4. The system auto-calculates late fees.
  5. Pay through electronic cash ledger.
  6. File return after payment.

If the fine under Rule 59 is applied, it will also appear as an additional liability in the portal.

8. Key Mistakes Businesses Should Avoid

  • Assuming late filing is harmless: Now penalties are much higher.
  • Ignoring GSTR-1 while filing GSTR-3B: Both must be in sync.
  • Not reconciling ITC: Mismatches lead to notices and fines.
  • Delaying nil returns: Even if no business, file to avoid fines.

9. FAQs

Q1. Is the ₹10,000 fine applicable for both GSTR-1 and GSTR-3B?
➡️ Primarily on GSTR-1 defaults, but non-filing of GSTR-3B can also attract notices and penalties.

Q2. Will the fine apply even if my turnover is below ₹1.5 crore?
➡️ Yes. The rule applies to all registered taxpayers irrespective of turnover.

Q3. Can late fees be waived under any special notification?
➡️ Sometimes the government waives late fees during amnesty schemes, but as of September 2025, no such waiver exists.

Q4. Can I claim Input Tax Credit if my supplier files late?
➡️ No. ITC is restricted unless the supplier files GSTR-1 correctly and on time.

10. Conclusion

The amendment to Rule 59 in September 2025 significantly increases the cost of GST non-compliance. A late fee that was earlier limited to a few hundred rupees can now escalate to ₹10,000+ per return. Small businesses should therefore prioritize timely filing, reconcile sales and purchases, and avoid mismatches.

👉 File your returns today at the official GST Portal.

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