GST Amnesty Scheme: Eligibility, Benefits, and Challenges

The GST Amnesty Scheme provides relief to taxpayers who missed filing certain GST returns or whose registrations were cancelled. It allows waiver or reduction of interest and late fees, aiming to reduce litigation and promote compliance.

What is the GST Amnesty Scheme?

The scheme was initially introduced for pending GSTR-3B returns from July 2017 to September 2018, with extensions provided later. It has been reintroduced multiple times:

2021: CBIC reopened the scheme for pending GSTR-3B returns from July 2017 to April 2021.
2023: GST Council recommended extending relief to GSTR-4, GSTR-9, and GSTR-10, and allowed revocation of cancelled registrations.
2024: Section 128A came into effect from 1st November 2024, providing waiver of interest and penalty for notices issued under Section 73 of CGST Act for FY 2017-18, 2018-19, and 2019-20.

Key Point: No refund is available if interest or penalty has already been paid.

Eligibility

Taxpayers who have pending returns for past periods (GSTR-3B, GSTR-4, GSTR-9, GSTR-10).
Taxpayers whose GST registrations were cancelled but seek revocation.
Taxpayers who have received notices under Section 73 for past financial years.

Benefits of GST Amnesty Scheme

Waiver/Reduction of Late Fees:
- GSTR-4: Maximum ₹500 per return (nil returns have no fee)
- GSTR-9: Maximum ₹20,000 (₹10,000 each for CGST & SGST)
- GSTR-10: Maximum ₹1,000 (₹500 each for CGST & SGST)
Waiver of Interest and Penalty under Section 128A for certain past periods.
Revocation of Cancelled GST Registrations with extended time for filing.
Reduction in Litigation: Encourages closure of disputes without legal proceedings.

Key Notifications under 2023 Amnesty Scheme

Notification	Form/Action	Who Can Avail	Benefits	Last Date
02/2023	GSTR-4 (Quarterly/Annual)	Composition taxpayers with pending GSTR-4 (Jul 2017 – Mar 2019 / FY 2019-20 to 2021-22)	Late fee capped at ₹500 per return; Nil returns exempt	30th June 2023
03/2023	GST REG-21	Taxpayers with cancelled GST registration due to non-filing / non-operation	Extended period to file REG-21 after clearing pending returns with tax, interest, late fee	30th June 2023
06/2023	Pending GST returns attracting Sec 62	Defaulting taxpayers	Deemed withdrawal of assessment order under Sec 62, even if appeal filed	30th June 2023
07/2023	GSTR-9 (Annual Return)	Regular taxpayers for FY 2017-18 to 2021-22	Late fee capped at ₹20,000; excess waived	30th June 2023
08/2023	GSTR-10 (Final Return)	Taxpayers with cancelled registration	Late fee capped at ₹1,000; excess waived	30th June 2023

Challenges

Taxpayers must pay any applicable tax along with pending returns to avail amnesty benefits.
Amnesty benefits may not cover all interest or penalties if already paid.
Proper documentation and filing within the specified period is crucial.

GST Amnesty Scheme 2021: Validity, Benefits, and Late Fee Relief

The GST Amnesty Scheme 2021 was introduced to help taxpayers clear pending GSTR-3B returns for periods between July 2017 and April 2021 with reduced compliance burden and late fees.

Validity

Initial Deadline: 1st June 2021 to 31st August 2021 (CBIC Notification No. 19/2021).
Extended Deadline: Up to 30th November 2021 (CBIC Notification No. 33/2021).

Implication: Taxpayers with pending GSTR-3B returns during the specified periods could file on or before 30th November 2021 to avail of the benefits under the scheme.

Benefits

Late Fee Relief:
- Maximum late fee per GSTR-3B with tax liability: ₹1,000 (₹500 CGST + ₹500 SGST).
- Maximum late fee per nil GSTR-3B return: ₹500 (₹250 CGST + ₹250 SGST).
Filing Flexibility: Taxpayers can file pending returns even if earlier periods were not filed, as long as all previous returns are submitted in sequence.
Business Continuity: Helps prevent GST registration cancellation due to non-filing of 6 consecutive months or 3 consecutive quarters, ensuring smooth business operations and maintaining credibility with GST-registered clients.
Economic Relief: Reduces financial burden, especially for businesses impacted by COVID-19 lockdowns and economic slowdown.

Example of Late Fee Calculation

Scenario: XYZ & Co has not filed GSTR-3B for January 2021 (due 20th Feb 2021).
Delay: 163 days, which would normally attract ₹8,150 as per standard late fee (₹50/day).
Under Amnesty Scheme: Late fee capped at ₹1,000.
Payment Required: ₹1,000 (late fee) + applicable tax liability and interest.

GST Amnesty Scheme: Filing Issues, Challenges, and Resolutions

The GST Amnesty Scheme offers relief to taxpayers with pending returns, but practical implementation may lead to technical issues, legal gaps, and compliance challenges. Here’s a detailed breakdown:

1. Resolution for Technical Issues While Filing GST Amnesty Application

Taxpayers filing the GST amnesty application may face system-related issues. The GSTN advisory dated 11th June 2025 provides the following solutions:

Steps to Resolve Common Filing Issues:

Demand Order Entry:
- Select ‘No’ for “Whether the demand order is issued through GST portal.”
- Enter the order number with prefix ‘ONL’.
  - Example: If the order number is ABCDE12345X1Z2 → enter as ONLABCDE12345X1Z2.
  - Without the prefix, the system treats it as a manual filing.
Basic Details:
- Select your mobile number and email ID from the dropdown.
- Manually fill other editable details like order details, payment details, and demand information.
Payment of Demanded Tax:
- Using DRC-03: Furnish payment details in Table-4.
- Payment towards demand: Upload payment details separately (cannot be entered in Table-4).

2. Challenges and Issues Under the GST Amnesty Scheme

No Relaxation in Interest Dues:
- Amnesty scheme only relaxes maximum late fees.
- Interest on pending tax liability is not waived.
Non-Admissibility of Input Tax Credit (ITC):
- ITC on past periods cannot be claimed while filing under the amnesty scheme.
- Legal provisions restrict claiming ITC after the due date of GSTR-3B or annual return for that financial year.
- Example: For FY 2019-20, ITC on a September 2020 invoice could be claimed by 20th October 2020 (GSTR-3B due date) or 31st December 2020 (annual return). Amnesty scheme does not extend this ITC claim period.
No Relief for GSTR-1 Late Filing:
- GSTR-1 is not covered under the scheme.
- Taxpayers must still file GSTR-1 for the same period separately.
Revocation of Cancelled GST Registration:
- Pending GSTR-3B cannot be filed without an active GSTIN.
- CBIC extended the time to apply for revocation of cancelled GSTIN up to 30th September 2021 (Notification 34/2021).

3. Suggested Solutions for Issues

Expand Scope: Include GSTR-1, GSTR-9, and GSTR-10 under the scheme to cover all pending returns.
Allow ITC Claims: Permit Input Tax Credit claims for past periods where the statutory time limit has expired, with options to revise returns.
Simplify Filing Process: Ensure smooth system interface for taxpayers to input demand order and payment details.
Legal Clarifications: Address ambiguities in notices and ensure taxpayers receive full benefits without technical barriers.

Conclusion: While the GST Amnesty Scheme is a major relief for pending returns, practical and legal issues remain. Taxpayers must carefully follow filing instructions, and the government should consider legal amendments and system enhancements to maximize the scheme’s effectiveness.

FAQs on GST Amnesty Scheme

How do I apply for the GST Amnesty Scheme?

To apply, eligible taxpayers must log in to the GST portal. Complete and file all pending returns, such as GSTR-3B or GSTR-9, and make the necessary payments with the reduced penalty under the scheme. Detailed instructions are available under the Amnesty Scheme guidelines on the GST portal.

Who qualifies for the GST Amnesty Scheme?

Businesses or individuals with pending GST returns or appeals, such as those who missed filing for certain tax periods, are generally eligible. Taxpayers must have tax dues or pending returns to benefit from the scheme.

What is the GST Amnesty Scheme for appeals?

The Amnesty Scheme provides relief on pending GST appeals by reducing or waiving penalties. Taxpayers with ongoing GST-related appeals can settle disputes early by paying the tax dues under the scheme.

What is the late fee reduction under the GST Amnesty Scheme?

Late fee reductions vary depending on the type of pending return and the period of delay. The scheme offers substantial reductions, making it easier for taxpayers to clear overdue returns.

Does the Amnesty Scheme apply to GSTR-9 (Annual Returns)?

Yes. Taxpayers who missed filing GSTR-9 may benefit from reduced or waived late fees, provided they file the returns within the Amnesty Scheme period.

Can I pay GST dues in installments under the Amnesty Scheme?

Yes. Taxpayers facing financial difficulties may apply for installment payments through the GST portal or their jurisdictional GST office.

Is ITC (Input Tax Credit) affected under the Amnesty Scheme?

No. ITC claims remain intact. Taxpayers can still claim eligible input tax credit while paying reduced penalties under the scheme.

Can a taxpayer apply if the GST return is already under scrutiny?

Yes. Even if returns are under audit or scrutiny, taxpayers can settle dues and benefit from reduced penalties under the Amnesty Scheme.

Is there a deadline to apply for the GST Amnesty Scheme?

Yes. The scheme is available for a specific period, which is notified by the government. Returns and payments must be completed within this period to avail benefits.

Are interest charges waived under the GST Amnesty Scheme?

The scheme primarily focuses on reducing penalties and late fees. Interest on unpaid taxes may still apply, depending on the scheme guidelines.

Can the Amnesty Scheme be applied to both CGST and SGST dues?

Yes. The scheme applies to central (CGST) and state (SGST/UTGST) dues, including pending interest, late fees, and penalties.

Is the Amnesty Scheme applicable for taxpayers under the Composition Scheme?

Yes. Even composition taxpayers with pending returns can benefit from the scheme if they meet eligibility criteria.

Can businesses settle multiple pending periods under the Amnesty Scheme?

Yes. Taxpayers can file all pending returns and settle dues for multiple tax periods under a single application.

How do I know if my GST dues are eligible under the Amnesty Scheme?

Eligible dues are usually listed in the GST portal under the Amnesty Scheme section. Taxpayers can check pending returns and appeals to determine eligibility.

GST Amnesty Scheme: Eligibility, Benefits, and Challenges

GST Amnesty Scheme: Eligibility, Benefits, and Challenges