Filing of SPL-01 and SPL-02 Where Payment is Made Through GSTR-3B

Filing of SPL-01 and SPL-02 Where Payment is Made Through GSTR-3B. On June 12th, 2025, the GSTN (Goods and Services Tax Network) released a advisory concerning the filing of amnesty applications in Form SPL-01 and SPL-02 under Section 128A of the CGST Act, 2017. This advisory addresses the technical challenges faced by taxpayers during the application process and provides clarifications for smooth filing. The guidance has significant implications for taxpayers seeking relief under the GST amnesty scheme, especially those who have made payments via GSTR-3B, demand orders, or pre-deposit methods.
What is Section 128A of the CGST Act, 2017? 
Section 128A provides an amnesty scheme for taxpayers to file pending returns and comply with past GST liabilities with a reduced penalty. It encourages voluntary compliance by allowing waiver of late fees and penalties under specified circumstances. Taxpayers opting for this scheme must submit their applications using Form SPL-01 or SPL-02, depending on the nature of their case.
Technical Glitches in Table 4 of SPL Forms
The GSTN has identified a recurring technical issue in Table 4 of the SPL-01 and SPL-02 forms. Specifically, the portal sometimes fails to auto-populate payment details correctly. This discrepancy creates confusion and apprehension among taxpayers, particularly when they have already made payments through valid means such as GSTR-3B returns or other payment functionalities available on the GST portal.
Key Scenarios Where Auto-Population Fails
The advisory outlines three key scenarios where auto-population of payment details in the forms may not work correctly:

Payments Made Through the "Payment Towards Demand Order" Functionality: Taxpayers who have made payments directly against a demand raised by the GST department using this portal functionality may find that these details are not auto-filled in Table 4 of the SPL form.

Pre-Deposit Amount Details: In appeal cases or demand notices, taxpayers often deposit a pre-decided percentage of the liability as a pre-deposit. These payments are sometimes omitted or misrepresented in the auto-populated fields.

Payment Made Through GSTR-3B: One of the most common methods of making tax payments is through filing of GSTR-3B. Despite this, the system may not reflect such payments accurately in the SPL-01 or SPL-02 forms.

GST Portal Allows Filing Despite Mismatches
The most reassuring part of the advisory is that the GST portal does not restrict the filing of SPL-01 or SPL-02 even if there is a mismatch or incomplete auto-population of payment and demand data. Taxpayers can still go ahead with submitting their applications. This is a critical relief for those facing system-related limitations, ensuring they are not penalized due to portal inefficiencies.
Recommended Action: Upload Supporting Documents
To compensate for the system’s inability to auto-populate payment details, GSTN strongly advises taxpayers to upload relevant supporting documents along with the online application. These documents may include:

Payment challans

Demand orders

GSTR-3B filing acknowledgments

Screenshots from the GST portal reflecting payment status

Any other payment confirmations

These documents will assist the jurisdictional officer in verifying the applicant’s claims and ensure a smooth processing of the amnesty application.
Jurisdictional Officer’s Role in Verification
Once the SPL application is submitted along with the attachments, the jurisdictional officer reviews the documents and validates the claims made by the taxpayer. The accuracy of the payment information plays a crucial role in the acceptance of the amnesty request. Taxpayers are advised to ensure that all information uploaded is legible, clear, and corresponds exactly to the declared liability.
Why This Advisory Matters to Taxpayers
Many taxpayers depend on the system to automatically fill in their financial data during return filings. However, system glitches can hinder compliance and delay submissions. This advisory comes as a relief to taxpayers who may have feared rejection of their applications due to such issues. It also clarifies the GSTN's intent to encourage compliance rather than penalize unintentional mistakes arising from technical limitations.
Implications for Future GST Amnesty Filings
This update sets a precedent for future filings under any relief schemes. Taxpayers are advised to:

Keep records of all payments made

Cross-check the data auto-filled in forms

Attach all relevant documents while filing applications

Keep a communication trail with jurisdictional officers for reference

Conclusion
The June 12th, 2025 advisory by GSTN reflects the government’s flexible approach towards encouraging taxpayer compliance, especially under the amnesty provisions of Section 128A. By allowing filings despite auto-population errors and urging supporting documentation uploads, GSTN has enabled smoother processing of SPL-01 and SPL-02 forms. Taxpayers must act responsibly by submitting clear documentation to avoid delays and ensure successful application processing.
Frequently Asked Questions (FAQs)
Q1. What is Form SPL-01 and SPL-02 used for?
Ans. These forms are used to apply for amnesty under Section 128A of the CGST Act, 2017 for waiver or reduction of penalties and late fees for past non-compliances.
Q2. What does Table 4 in the SPL forms capture?
 Ans. Table 4 captures details of the payment made towards tax demand or liability. It includes information on the mode and amount of payment.
Q3. What if my payment details are not showing correctly in Table 4?
 Ans. You can still file the application. The GST portal allows submission even if the payment and demand details do not match.
Q4. What supporting documents should I upload?
 Ans. You should upload challans, GSTR-3B acknowledgements, demand order copies, and any other relevant proof of payment.
Q5. Will my application be rejected if the system fails to auto-populate my payment?
 Ans. No. Your application will not be rejected solely due to auto-population errors. However, ensure proper supporting documentation is attached.
Q6. Who verifies the details after I file the SPL application?
 Ans. The jurisdictional officer assigned to your GST registration verifies the documents and approves the application.
Q7. What is a pre-deposit in GST?
 Ans. A pre-deposit is a partial payment made as a condition for filing an appeal against a tax demand or order.
Q8. Is GSTR-3B payment sufficient proof for the SPL application?
 Ans. Yes, if you have paid the liability through GSTR-3B, include proof like acknowledgment or ledger entries.
Q9. Can I file SPL-01 without making full payment of tax?
 Ans. No, you must make the required payment as per the scheme and attach proof along with your application.
Q10. Where can I get help if I still face issues while filing SPL-01 or SPL-02?
 Ans. You can contact the GST Helpdesk or approach your jurisdictional officer for guidance.

On June 12th, 2025, the GSTN (Goods and Services Tax Network) released a advisory concerning the filing of amnesty applications in Form SPL-01 and SPL-02 under Section 128A of the CGST Act, 2017. This advisory addresses the technical challenges faced by taxpayers during the application process and provides clarifications for smooth filing. The guidance has significant implications for taxpayers seeking relief under the GST amnesty scheme, especially those who have made payments via GSTR-3B, demand orders, or pre-deposit methods.

What is Section 128A of the CGST Act, 2017?

Section 128A provides an amnesty scheme for taxpayers to file pending returns and comply with past GST liabilities with a reduced penalty. It encourages voluntary compliance by allowing waiver of late fees and penalties under specified circumstances. Taxpayers opting for this scheme must submit their applications using Form SPL-01 or SPL-02, depending on the nature of their case.

Technical Glitches in Table 4 of SPL Forms

The GSTN has identified a recurring technical issue in Table 4 of the SPL-01 and SPL-02 forms. Specifically, the portal sometimes fails to auto-populate payment details correctly. This discrepancy creates confusion and apprehension among taxpayers, particularly when they have already made payments through valid means such as GSTR-3B returns or other payment functionalities available on the GST portal.

Key Scenarios Where Auto-Population Fails

The advisory outlines three key scenarios where auto-population of payment details in the forms may not work correctly:

Payments Made Through the "Payment Towards Demand Order" Functionality: Taxpayers who have made payments directly against a demand raised by the GST department using this portal functionality may find that these details are not auto-filled in Table 4 of the SPL form.
Pre-Deposit Amount Details: In appeal cases or demand notices, taxpayers often deposit a pre-decided percentage of the liability as a pre-deposit. These payments are sometimes omitted or misrepresented in the auto-populated fields.
Payment Made Through GSTR-3B: One of the most common methods of making tax payments is through filing of GSTR-3B. Despite this, the system may not reflect such payments accurately in the SPL-01 or SPL-02 forms.

GST Portal Allows Filing Despite Mismatches

The most reassuring part of the advisory is that the GST portal does not restrict the filing of SPL-01 or SPL-02 even if there is a mismatch or incomplete auto-population of payment and demand data. Taxpayers can still go ahead with submitting their applications. This is a critical relief for those facing system-related limitations, ensuring they are not penalized due to portal inefficiencies.

Recommended Action: Upload Supporting Documents

To compensate for the system’s inability to auto-populate payment details, GSTN strongly advises taxpayers to upload relevant supporting documents along with the online application. These documents may include:

Payment challans
Demand orders
GSTR-3B filing acknowledgments
Screenshots from the GST portal reflecting payment status
Any other payment confirmations

These documents will assist the jurisdictional officer in verifying the applicant’s claims and ensure a smooth processing of the amnesty application.

Jurisdictional Officer’s Role in Verification

Once the SPL application is submitted along with the attachments, the jurisdictional officer reviews the documents and validates the claims made by the taxpayer. The accuracy of the payment information plays a crucial role in the acceptance of the amnesty request. Taxpayers are advised to ensure that all information uploaded is legible, clear, and corresponds exactly to the declared liability.

Why This Advisory Matters to Taxpayers

Many taxpayers depend on the system to automatically fill in their financial data during return filings. However, system glitches can hinder compliance and delay submissions. This advisory comes as a relief to taxpayers who may have feared rejection of their applications due to such issues. It also clarifies the GSTN's intent to encourage compliance rather than penalize unintentional mistakes arising from technical limitations.

Implications for Future GST Amnesty Filings

This update sets a precedent for future filings under any relief schemes. Taxpayers are advised to:

Keep records of all payments made
Cross-check the data auto-filled in forms
Attach all relevant documents while filing applications
Keep a communication trail with jurisdictional officers for reference

Conclusion

The June 12th, 2025 advisory by GSTN reflects the government’s flexible approach towards encouraging taxpayer compliance, especially under the amnesty provisions of Section 128A. By allowing filings despite auto-population errors and urging supporting documentation uploads, GSTN has enabled smoother processing of SPL-01 and SPL-02 forms. Taxpayers must act responsibly by submitting clear documentation to avoid delays and ensure successful application processing.

Frequently Asked Questions (FAQs)

Q1. What is Form SPL-01 and SPL-02 used for?

Ans. These forms are used to apply for amnesty under Section 128A of the CGST Act, 2017 for waiver or reduction of penalties and late fees for past non-compliances.

Q2. What does Table 4 in the SPL forms capture?

Ans. Table 4 captures details of the payment made towards tax demand or liability. It includes information on the mode and amount of payment.

Q3. What if my payment details are not showing correctly in Table 4?

Ans. You can still file the application. The GST portal allows submission even if the payment and demand details do not match.

Q4. What supporting documents should I upload?

Ans. You should upload challans, GSTR-3B acknowledgements, demand order copies, and any other relevant proof of payment.

Q5. Will my application be rejected if the system fails to auto-populate my payment?

Ans. No. Your application will not be rejected solely due to auto-population errors. However, ensure proper supporting documentation is attached.

Q6. Who verifies the details after I file the SPL application?

Ans. The jurisdictional officer assigned to your GST registration verifies the documents and approves the application.

Q7. What is a pre-deposit in GST?

Ans. A pre-deposit is a partial payment made as a condition for filing an appeal against a tax demand or order.