Filing of Amnesty Applications under Section 128A of the CGST Act

Filing of Amnesty Applications under Section 128A of the CGST Act. The Goods and Services Tax Network (GSTN) has released an important advisory for taxpayers who are facing difficulties while filing amnesty applications under Section 128A of the Central Goods and Services Tax (CGST) Act, 2017. This advisory, dated June 11, 2025, addresses the issues related to technical glitches on the GST portal and outlines an alternate procedure to ensure that taxpayers are not deprived of the benefits of the amnesty scheme.
Background of the Advisory
As of June 8, 2025, a total of 3,02,658 waiver applications have been successfully filed through Forms SPL-01 and SPL-02 on the GST portal. These applications are part of the ongoing amnesty scheme provided under Section 128A of the CGST Act. However, despite the significant number of filings, it has come to light that several taxpayers are facing technical issues while attempting to submit their waiver applications online.
Various trade associations and taxpayers have submitted representations to the GSTN, requesting an alternate mechanism for filing the amnesty applications due to the technical difficulties being experienced on the GST portal. In response, the GSTN has issued this advisory, suggesting an alternate step-wise method that can be adopted by such taxpayers.
What is Section 128A of the CGST Act?
Section 128A of the CGST Act provides relief in the form of amnesty to taxpayers by allowing them to apply for waiver of late fees, penalties, or interest under specific circumstances. The scheme has been introduced to help taxpayers who have failed to file their GST returns on time and are now looking to regularize their compliance status without facing the full burden of penalties.
The amnesty scheme is a time-bound window and is meant to reduce the litigation burden, improve tax compliance, and provide relief to genuine taxpayers who may have defaulted due to various reasons.
Existing Filing Status under the Amnesty Scheme
According to the GSTN's report, over 3 lakh applications have been filed using the prescribed forms SPL-01 and SPL-02. This indicates a positive response from taxpayers across the country. However, a segment of taxpayers is still struggling with system-generated errors or technical glitches on the GST portal, which is restricting them from filing the waiver application within the stipulated timeline.
Common Technical Issues Being Faced
Some of the common technical problems reported include:

Portal errors during final submission

Non-availability of correct return periods

Inability to download or upload relevant forms

Session time-outs or server errors

Due to these issues, many taxpayers are unable to complete the application process despite repeated attempts. These problems have prompted the GSTN to step in and provide a user-friendly alternative.
Alternate Mechanism for Filing
In order to assist those facing technical glitches, the GSTN has suggested a step-wise alternate filing procedure. Taxpayers are advised to follow the instructions provided in a detailed PDF document, which can be accessed from the official GST portal:
Click here to view the steps
This PDF guide contains screenshots, step-by-step instructions, and additional tips to help users navigate the process and ensure successful filing of the waiver application.
Steps to Be Taken by Affected Taxpayers

Access the Advisory PDF: Open the link provided by the GSTN to view the alternative steps for filing.

Follow the Instructions: Carefully go through each step mentioned in the document. It includes detailed information on how to handle errors and complete the filing process.

Capture Screenshots (if needed): In case the issue persists even after following the steps, take screenshots of the error messages.

Raise a Complaint on GST Self-Service Portal: If the technical difficulty remains unresolved, raise a grievance immediately on the GST Self-Service Portal: https://selfservice.gstsystem.in

Raising a timely complaint ensures that the issue is documented and can be resolved by the technical support team.
Importance of Timely Filing
Taxpayers must note that the amnesty scheme is time-sensitive. The GSTN has not extended the deadline beyond the original window. Delayed submissions may result in the taxpayer losing the benefit of the waiver and becoming liable for full penalties and interest under the Act.
Filing within the prescribed timeline also helps avoid further legal complications, including show cause notices and recovery proceedings.
Role of Trade Bodies
Trade bodies and industry associations have played a crucial role in bringing the problems to the attention of GSTN. Their proactive representations led to the release of this advisory. Taxpayers are encouraged to stay connected with such associations for real-time updates and assistance.
GST Self-Service Portal: A Help Desk for Taxpayers
The GST Self-Service Portal is a user-friendly platform where taxpayers can log complaints, check the status of grievances, and get responses from the support team. It is important to provide accurate details and attach relevant screenshots when submitting a complaint.
Steps to use the portal:

Visit https://selfservice.gstsystem.in

Select the nature of the complaint

Fill in the required details

Upload supporting documents/screenshots

Submit the form and note the reference number

Conclusion
The advisory issued by the GSTN is a proactive step to ensure that genuine taxpayers are not deprived of the amnesty benefits due to technical challenges. With more than 3 lakh applications already filed, it is essential for the remaining taxpayers to act swiftly, use the alternate mechanism if needed, and raise complaints promptly in case of unresolved issues. The step-by-step guide and help desk support are designed to make the process smoother and more accessible.
Taxpayers should make the most of this opportunity under Section 128A of the CGST Act and ensure compliance with GST norms while availing the benefit of fee and penalty waiver.
Frequently Asked Questions (FAQs)
Q1. What is the purpose of the advisory issued on June 11, 2025?
Ans. The advisory aims to help taxpayers facing technical issues while filing amnesty applications under Section 128A of the CGST Act on the GST portal. It offers an alternate filing procedure and guidance to ensure timely compliance.
Q2. What is Section 128A of the CGST Act?
Ans. Section 128A allows taxpayers to apply for waiver of late fees, interest, or penalties under specific conditions, as part of a government-declared amnesty scheme.
Q3. How many applications have been filed under the amnesty scheme as of June 8, 2025?
Ans. A total of 3,02,658 waiver applications have been filed using Forms SPL-01 and SPL-02.
Q4. What are some common issues taxpayers are facing on the GST portal?
Ans. Issues include system errors, missing return periods, upload/download failures, and server timeouts.
Q5. Where can I find the alternate steps for filing my application?
Ans. Taxpayers can view the alternate filing procedure in this document: https://tutorial.gst.gov.in/downloads/news/link_data.pdf
Q6. What should I do if the alternate steps also don’t work?
Ans. You should immediately raise a complaint on the GST Self-Service Portal: https://selfservice.gstsystem.in
Q7. Is there any deadline for filing the amnesty application?
Ans. Yes, the amnesty scheme is time-bound. Taxpayers must submit their applications before the last date as notified by GSTN.
Q8. Can I file the amnesty application manually or offline?
Ans. No. The application must be submitted online via the GST portal or by following the alternate online method provided in the advisory.
Q9. Do I need to submit any physical documents for the waiver?
Ans. No physical submission is required. All relevant documents and information must be uploaded online.
Q10. Will the benefit be available if I fail to file the application before the deadline?
Ans. No. If you miss the deadline, you may not be eligible for the waiver benefits and will have to pay the applicable late fees, penalties, or interest.

The Goods and Services Tax Network (GSTN) has released an important advisory for taxpayers who are facing difficulties while filing amnesty applications under Section 128A of the Central Goods and Services Tax (CGST) Act, 2017. This advisory, dated June 11, 2025, addresses the issues related to technical glitches on the GST portal and outlines an alternate procedure to ensure that taxpayers are not deprived of the benefits of the amnesty scheme.

Background of the Advisory

As of June 8, 2025, a total of 3,02,658 waiver applications have been successfully filed through Forms SPL-01 and SPL-02 on the GST portal. These applications are part of the ongoing amnesty scheme provided under Section 128A of the CGST Act. However, despite the significant number of filings, it has come to light that several taxpayers are facing technical issues while attempting to submit their waiver applications online.

Various trade associations and taxpayers have submitted representations to the GSTN, requesting an alternate mechanism for filing the amnesty applications due to the technical difficulties being experienced on the GST portal. In response, the GSTN has issued this advisory, suggesting an alternate step-wise method that can be adopted by such taxpayers.

What is Section 128A of the CGST Act?

Section 128A of the CGST Act provides relief in the form of amnesty to taxpayers by allowing them to apply for waiver of late fees, penalties, or interest under specific circumstances. The scheme has been introduced to help taxpayers who have failed to file their GST returns on time and are now looking to regularize their compliance status without facing the full burden of penalties.

The amnesty scheme is a time-bound window and is meant to reduce the litigation burden, improve tax compliance, and provide relief to genuine taxpayers who may have defaulted due to various reasons.

Existing Filing Status under the Amnesty Scheme

According to the GSTN's report, over 3 lakh applications have been filed using the prescribed forms SPL-01 and SPL-02. This indicates a positive response from taxpayers across the country. However, a segment of taxpayers is still struggling with system-generated errors or technical glitches on the GST portal, which is restricting them from filing the waiver application within the stipulated timeline.

Common Technical Issues Being Faced

Some of the common technical problems reported include:

Portal errors during final submission
Non-availability of correct return periods
Inability to download or upload relevant forms
Session time-outs or server errors

Due to these issues, many taxpayers are unable to complete the application process despite repeated attempts. These problems have prompted the GSTN to step in and provide a user-friendly alternative.

Alternate Mechanism for Filing

In order to assist those facing technical glitches, the GSTN has suggested a step-wise alternate filing procedure. Taxpayers are advised to follow the instructions provided in a detailed PDF document, which can be accessed from the official GST portal:

Click here to view the steps

This PDF guide contains screenshots, step-by-step instructions, and additional tips to help users navigate the process and ensure successful filing of the waiver application.

Steps to Be Taken by Affected Taxpayers

Access the Advisory PDF: Open the link provided by the GSTN to view the alternative steps for filing.
Follow the Instructions: Carefully go through each step mentioned in the document. It includes detailed information on how to handle errors and complete the filing process.
Capture Screenshots (if needed): In case the issue persists even after following the steps, take screenshots of the error messages.
Raise a Complaint on GST Self-Service Portal: If the technical difficulty remains unresolved, raise a grievance immediately on the GST Self-Service Portal: https://selfservice.gstsystem.in

Raising a timely complaint ensures that the issue is documented and can be resolved by the technical support team.

Importance of Timely Filing

Taxpayers must note that the amnesty scheme is time-sensitive. The GSTN has not extended the deadline beyond the original window. Delayed submissions may result in the taxpayer losing the benefit of the waiver and becoming liable for full penalties and interest under the Act.

Filing within the prescribed timeline also helps avoid further legal complications, including show cause notices and recovery proceedings.

Role of Trade Bodies

Trade bodies and industry associations have played a crucial role in bringing the problems to the attention of GSTN. Their proactive representations led to the release of this advisory. Taxpayers are encouraged to stay connected with such associations for real-time updates and assistance.

GST Self-Service Portal: A Help Desk for Taxpayers

The GST Self-Service Portal is a user-friendly platform where taxpayers can log complaints, check the status of grievances, and get responses from the support team. It is important to provide accurate details and attach relevant screenshots when submitting a complaint.

Steps to use the portal:

Visit https://selfservice.gstsystem.in
Select the nature of the complaint
Fill in the required details
Upload supporting documents/screenshots
Submit the form and note the reference number

Conclusion

The advisory issued by the GSTN is a proactive step to ensure that genuine taxpayers are not deprived of the amnesty benefits due to technical challenges. With more than 3 lakh applications already filed, it is essential for the remaining taxpayers to act swiftly, use the alternate mechanism if needed, and raise complaints promptly in case of unresolved issues. The step-by-step guide and help desk support are designed to make the process smoother and more accessible.

Taxpayers should make the most of this opportunity under Section 128A of the CGST Act and ensure compliance with GST norms while availing the benefit of fee and penalty waiver.

Frequently Asked Questions (FAQs)

Q1. What is the purpose of the advisory issued on June 11, 2025?

Ans. The advisory aims to help taxpayers facing technical issues while filing amnesty applications under Section 128A of the CGST Act on the GST portal. It offers an alternate filing procedure and guidance to ensure timely compliance.

Q2. What is Section 128A of the CGST Act?

Ans. Section 128A allows taxpayers to apply for waiver of late fees, interest, or penalties under specific conditions, as part of a government-declared amnesty scheme.

Q3. How many applications have been filed under the amnesty scheme as of June 8, 2025?

Ans. A total of 3,02,658 waiver applications have been filed using Forms SPL-01 and SPL-02.

Q4. What are some common issues taxpayers are facing on the GST portal?

Ans. Issues include system errors, missing return periods, upload/download failures, and server timeouts.

Q5. Where can I find the alternate steps for filing my application?

Ans. Taxpayers can view the alternate filing procedure in this document: https://tutorial.gst.gov.in/downloads/news/link_data.pdf

Q6. What should I do if the alternate steps also don’t work?

Ans. You should immediately raise a complaint on the GST Self-Service Portal: https://selfservice.gstsystem.in

Q7. Is there any deadline for filing the amnesty application?

Ans. Yes, the amnesty scheme is time-bound. Taxpayers must submit their applications before the last date as notified by GSTN.

Q8. Can I file the amnesty application manually or offline?

Ans. No. The application must be submitted online via the GST portal or by following the alternate online method provided in the advisory.

Q9. Do I need to submit any physical documents for the waiver?

Ans. No physical submission is required. All relevant documents and information must be uploaded online.

Q10. Will the benefit be available if I fail to file the application before the deadline?

Ans. No. If you miss the deadline, you may not be eligible for the waiver benefits and will have to pay the applicable late fees, penalties, or interest.