The Government has introduced last-minute relief measures under the GST Amnesty Scheme just days before the critical March 31, 2025 deadline for payment of outstanding tax dues. Through Notification No. 11/2025–Central Tax, the Ministry of Finance has amended Rule 164 of CGST Rules, aiming to address taxpayers’ practical difficulties in availing the amnesty relief for FY 2017-18 to 2019-20.
This article breaks down the updates, legal implications, and how businesses can benefit.
🔹 Key Deadlines You Must Know
- March 31, 2025: Deadline to pay tax dues under the Amnesty Scheme
- June 30, 2025: Deadline to file application for waiver of interest and penalty
📊 What Has Changed Under the GST Amnesty Scheme?
1. Appeals for Mixed Tax Periods: Partial Withdrawal Now Allowed
Earlier, if a GST appeal covered both eligible and non-eligible periods (like FY 2017-18 to 2019-20 along with FY 2020-21), taxpayers had to withdraw the entire appeal to claim amnesty.
Amendment Relief: Under Rule 164(4) and Proviso to Rule 164(7), taxpayers can now partially withdraw the appeal—only for the eligible period. Appeals for remaining years can proceed as usual.
Legal Reference:
Notification No. 11/2025–Central Tax, dated March 27, 2025
2. Mode of Tax Payment: GSTR-3B Now Acceptable (Before Nov 1, 2024)
Initially, taxpayers were required to use FORM GST DRC-03 to pay outstanding dues. Many who paid via GSTR-3B faced issues claiming amnesty benefits.
Clarification Issued: Circular No. 248/05/2025 clarifies that payments made via GSTR-3B before November 1, 2024 will also be eligible for amnesty relief, subject to verification.
📓 Summary Table: Eligibility and Payment Mode
| Clause | Case Type | Payment Due By | Payment Mode | Application Form | Application Deadline |
|---|---|---|---|---|---|
| (a) | Notice u/s 73, no order | 31-03-2025 | DRC-03 | SPL-01 | 30-06-2025 |
| (b) | Order u/s 73, no appeal | 31-03-2025 | E-Liability Register | SPL-02 | 30-06-2025 |
| (c) | OIA passed, no tribunal | 31-03-2025 | E-Liability Register | SPL-02 | 30-06-2025 |
| 1st Proviso | Order u/s 74 changed to 73 | Within 6 months | E-Liability Register | SPL-02 | Within 6 months |
| 2nd Proviso | OIA revised by department | Within 3 months | E-Liability Register | SPL-02 | Within 3 months |
📆 What Business Owners Should Do Before March 31, 2025
- Review GST demands issued under Section 73 for FY 17-18 to 19-20.
- Check mode of past payments (GSTR-3B or DRC-03).
- Ensure payment by March 31, 2025 in proper format to avoid ineligibility.
- File SPL-01 or SPL-02 before June 30, 2025.