GST Amnesty Scheme: 4 Proven Ways To Get Late Fees Waiver

The Government of India implemented the GST Amnesty Scheme to enable taxpayers to pay the  past due money and the non-compliance matters under the Goods and Services Tax (GST)  law. The initiative is a relief measure in terms of interest, penalty, and late charges waiver that will  prompt business owners to normalize past defaults without the imposition of severe financial  implications. This paper will discuss the meaning of the GST Amnesty Scheme, its key  advantages, eligibility factors, and the process of applying step by step.

What is the GST Amnesty Scheme?  

GST Amnesty Scheme is a dedicated one-time concession scheme under which taxpayers are  permitted to clear their outstanding tax liabilities with huge concessions in the payment of  interest, penalty, or outstanding late charges. This scheme was implemented by the Central  Board of Indirect Taxes and Customs (CBIC) in Section 128A of the CGST act, which applies  primarily in the financial year 2017-18, 2018-19, and 2019-20.

The scheme enforces cases  where the demands have been increased under Section 73 of the CGST Act (non-fraudulent  cases). It also includes the instances when the returns were not submitted, the GST registrations  were cancelled on the grounds of non-compliance, or when the taxpayers desire to settle the old  disputes. Simply put, it provides the taxpayers with an opportunity to settle their pending  payments by paying only the principal amount of tax and being relieved with waiving of late fees  and penalty charges.  

Key Advantages of the Amnesty Scheme 

1. Waiver of Interest and Penalty: The greatest advantage of the GST Amnesty Scheme is the  exemption or lessening of interests and penalties. These additional charges can be completely  relieved to taxpayers who will have paid their full taxes by March 31, 2025. This implies that  businesses are able to settle old closed cases by paying the principal tax amount without being  concerned with the high interest rate and penalties.   
                     
2. Pending Returns Late Fees Waive:. The waiver of late fees on old returns is another one of the  key highlights. During the initial years of implementation, many taxpayers failed to submit GST  returns either because they were confused or because they had technical problems. The Amnesty  scheme provides them with an opportunity to present pending returns at a low or fixed fee. Past  exceptions to amnesty have included: GSTR-3B Returns – The amount of late fees that can be  charged per return was reduced to 1000 (500 CGST + 500 SGST) during July 2017-April 2021.                                                                                                                                                                                                  GSTR-9 (Annual Return)- The late fee was remitted over 20000 in case of late filing. GSTR-10 (Final  Return) -Latest fee is limited to 1000 only. GSTR-4 (Composition Return) -Late fees cut down to 500,000 INR where non-nil returns and completely removed where nil returns. Small and medium  businesses can wipe off backlogs and reestablish compliance at minimal expense with this late fees waiver.                                       
3. Revocation of Past Assessment Orders: Where a taxpayer has made all outstanding returns  and paid taxes in accordance with this scheme, previous best-judgment assessments (orders  passed under Section 62 owing to a failure to make a return) can be automatically revoked. This  is a great relief to individuals whose estimated taxes were supposed to be paid because of  unfiled returns.                                                                                                  
4. Reinstatement of Cancelled GSTIN: Amnesty scheme also enables taxpayers, the registration of which has been revoked because of non-filing of returns, to request revocation of the  cancellation. Registration can be restored once pending returns are submitted and dues paid, so that the business could carry on legally under GST. 5. Reduction in Litigation The amnesty  scheme prevents the costs of appeals, notices, and litigation by both taxpayer and authorities  since voluntary compliance will be encouraged. It encourages good faith and delivers a smoother  tax administration. 
   

Eligibility Criteria

1. Eligible Taxpayers:  

The recipients of notices or orders in Section 73 (non-fraudulent tax demands). Taxpayers that desire to settle FY 2017-18, 2018-19, or 2019-20 demands. Those taxpayers whose registration  was cancelled as a result of non-filing of returns but who now want to reinstate.  

2. Not Eligible:                                           

Fraud, suppression, or misstatement cases under Section 74. Interest or penalties on self-assessment returns have not been returned. Already paid demands or those on which appeals have not  been withdrawn. Other Acts: Refund or import cases. 

Application: How to apply to the GST Amnesty Scheme 

The following is the procedure to be followed to claim relief under GST Amnesty Scheme: 

Step 1: Pay the Full Tax Amount:

Before paying the taxpayer any amount of principal tax due under the notice  or order under Section 73, he or she must first have to pay all the principal tax. The remuneration  is to be paid at or before March 31, 2025.  

Step 2: Request the Dismissal of a pending appeal or Write:

In case either appeal or a writ petition is  in progress on the same demand, it should be withdrawn prior to submitting the amnesty  application. During the application process, proof of withdrawal or withdrawal application should  be uploaded. 

Step 3: File Form GST SPL-02:

Eligible taxpayers should apply online on the GST portal by filling a Form GST SPL-02. It is a unique form of claiming the scheme benefits of waiver. This application is also due on June 30, 2025.  

Step 4: Add Supportive Documents:

Taxpayers should also include the following documents with the SPL-02 form: Proof of tax payment, a copy of the order / withdrawal application, and any other  documents that are necessary by the GST authorities.  

Step 5: Final assurance and Finalization:

After the checks and balances of the application have  been proven and accepted, the authorities will give a confirmation order waiving the interest that  should be charged, the penalty, or the late charges. The case will further be considered closed, and no additional appeal or recovery will be further made. Significant Things to keep in mind.

The  waiver does not include cases of fraud or misdeclaration, but only in Section 73 demands.  Before becoming eligible to the waiver, tax payers would have to pay the entire amount of tax.  After granting the amnesty, there can be no additional attempts to appeal on those matters. The  late fees waiver can only be taken on the basis of the pending returns being filed during the  amnesty.  

Conclusion  

The GST Amnesty Scheme is one silver lining of the taxpayers as they get a chance to clear old-time tax and disputes without meeting the huge penalties. Interest and penalties should be waived and reduced to make the small business and traders easier to get back on track and to prevent any future-related problems.

References:

[1] TaxTMI, “GST Amnesty/Waiver Scheme: Law and Conditions,” TaxTMI, June 2025. [Online].

Available: axtmi.com/article/detailed?id=14593

[2] Clear Tax, “GST Amnesty Scheme,” Clear Tax, August 2025. [Online].

Available: https://cleartax.in/s/gst-amnesty-scheme