Action Required by 31-03-2025: GST Amnesty Scheme Under Section 128A

ACTION REQUIRED ON OR BEFORE 31-03-2025 ON AMNESTY SCHEME UNDER SECTION 128A OF GST ACT, 2017 AS PER NEW AMENDMENT IN RULE 164 OF GST RULES, 2017

The Central Government, through Notification No. 11/2025 dated March 27, 2025, has introduced crucial amendments in Rule 164 of the Central Goods and Services Tax (CGST) Rules, 2017. These amendments primarily affect sub-rule (4) and sub-rule (7) of Rule 164 and have significant implications for taxpayers opting for the Amnesty Scheme under Section 128A of the CGST Act, 2017. The key changes introduced through this notification and their impact are discussed below.

1. Amendment to Sub-rule (4) of Rule 164 – Specified Period and Payment Obligation

As per the amended sub-rule (4) of Rule 164, an appellant who seeks to avail the benefits under Section 128A of the CGST Act, 2017, is now required to make the requisite tax payment only for the period covered under Section 128A. Specifically, the demand raised under Section 73 of the CGST Act for the tax period of July 2017 to March 2018, FY 2018-19, and FY 2019-20 must be settled to qualify for the amnesty benefits.

This clarification ensures that taxpayers are not burdened with demands for periods outside the amnesty period specified under Section 128A.

2. Explanation Inserted Under Rule 164(4) – Restriction on Refund Claims

The amendment also introduces a crucial explanation to Rule 164(4), which states:

• No refund shall be available for any tax, interest, or penalty that has already been discharged for the entire period prior to March 27, 2025 (the commencement date of the Central Goods and Services Tax (Second Amendment) Rules, 2025).
• This restriction applies in cases where a notice, statement, or order, as mentioned under sub-section (1) of Section 128A, includes a tax demand partially for the amnesty-covered period (July 2017 – March 2018, FY 2018-19, and FY 2019-20) and partially for a period beyond the amnesty coverage.

This amendment eliminates any possibility of taxpayers claiming a refund of amounts already paid for pre-amnesty tax periods.

3. Amendment to Sub-rule (7) of Rule 164 – Procedural Clarifications for Partial Appeal Withdrawal

The amendment to sub-rule (7) of Rule 164 provides a significant procedural change for taxpayers who wish to opt for the amnesty scheme but have pending appeals covering both amnesty and non-amnesty periods.

• A proviso has been inserted, allowing the taxpayer to intimate the appellate authority or Appellate Tribunal that they do not wish to pursue the appeal for the tax period covered under Section 128A.
• The appellate authority, upon receiving such an intimation, shall issue an order only for the non-amnesty period, as it deems just and proper.
• This process serves as a deemed withdrawal of appeal for the amnesty-covered period, as prescribed under sub-clause (3) of Section 128A.

This amendment significantly simplifies the process for taxpayers, ensuring that they can continue their appeals for non-amnesty periods while availing the benefits of waiver of interest and penalty for the amnesty-covered periods.

4. Practical Implications for Taxpayers

Taxpayers must take note of the following actions to comply with the new amendments:

i. Ensure payment of the specified tax demand for the period July 2017 – March 2018, FY 2018-19, and FY 2019-20 if opting for amnesty relief under Section 128A on or before 31-03-2025.

ii. File application in SPl-01 or spl-02 as the case may be online/offline as applicable on or before 30-06-2025.

(Please note at present there is no provision is available to file SPL-01 or SPL-02 for the partial period as per the amended Rule 164 of GST Rules, 2017as per Notification No: 11/2025 CTR.)

iii. File an intimation with the appellate authority/Appellate Tribunal if the appeal covers both amnesty and non-amnesty periods, to partially withdraw the appeal for the amnesty period.

iv. Await the order of the appellate authority for the non-amnesty period to determine the further course of action.

5. Draft letter for taxpayers seeking partial appeal withdrawal

To facilitate compliance, a draft letter format for intimation to the appellate authority/Appellate Tribunal regarding partial withdrawal of appeal under Section 128A of the CGST Act is enclosed/appended. Taxpayers may modify the letter as per their organization’s specific requirements.

Draft letter

Date…………..

Your Name/Company Name
Your Address
City, State, ZIP Code
GSTIN (if applicable)
Email ID……………. Contact Number

To,
The Designation of the Authority
Office Address
City, State, ZIP Code

Respected Sir/Madam

Subject: M/s………………….GSTN No…………….Intimation regarding payment under Amnesty Scheme and continuation of appeal for the other period-Reg

Reference:

1. Notice/Statement/Order No. …………………
2. Appeal No. and date………………., if applicable

With reference to the above-mentioned notice/order, we wish to submit that the demand raised therein pertains to multiple tax periods, including Tax demanded July 2017 – March 2018 FY 2018-19 FY 2019-20 is as under:

2. As per the newly inserted proviso to sub-rule (7) of Rule 164 of the CGST Rules, 2017, we hereby submit our intimation that we wish to avail the Amnesty Scheme under Section 128A for the tax period of July 2017 to March 2018, FY 2018-19, and FY 2019-20 and accordingly, we have made the necessary payment as required under the scheme.

3. The details of the payment made are as follows:

4. As per the proviso to Rule 164(7), instead of withdrawing the entire appeal, we hereby intimate that we do not wish to pursue the appeal for the period covered under the Amnesty Scheme, and accordingly, request your good office to take note of this intimation and pass necessary orders for the remaining tax period(s) which are beyond the scope of the Amnesty Scheme.

5. Furthermore, as per the explanation under Rule 164(7), this intimation shall be considered as a withdrawal of appeal for the period covered under the Amnesty Scheme in terms of Section 128A(3) of the CGST Act, 2017.

6. In view of the above, we kindly request your good office to take necessary action and issue an appropriate order confirming the partial withdrawal of the appeal and continue the appellate proceedings for the other periods not covered under the scheme. We will be submitting the required application in SPl-01/SPL-02 before the 30-06-2025 once the new provisions are made applicable in portal as prescribed the Department.

7. We are ready to provide any further clarification or documentation in this regard.

Thanking you.

Yours sincerely,
For ………………………

(Signature of the Authorsed person)
Designation……………….

Email ID
Contact Number

Enclosures:

1. Copy of Notice/Order inn Order/Order in Appeal.
2. Document evidencing payment as mentioned above.

Conclusion

The amendments introduced via Notification No. 11/2025 provide greater clarity on the scope and applicability of the Amnesty Scheme under Section 128A. These changes ensure that taxpayers opting for amnesty relief are only required to make payments for the prescribed periods and that appeal processes are streamlined for mixed-period demands. However, taxpayers must carefully assess their liabilities and consult with legal experts to ensure compliance with the revised provisions.

For further guidance, taxpayers may refer to official CBIC circulars and FAQs related to the implementation of these amendments.

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By : B. Venkateswaran, IRS., Assistant Commissioner Central GST(Retired),