Most Common GST Portal Issues and How to Fix Them

GST portal issues range from simple browser problems to complex data validation failures. Most GST common errors fall into four categories: login errors, OTP failures, return filing errors, and system-level errors.

Top GST Portal Errors and Suggested Solutions

These are the common GST problems, along with their solutions, as documented by the GSTN for return filing and portal usage.

Login And Access Errors

1. Invalid Username Or Password

Solution: Carefully enter your credentials and ensure they are typed correctly. In case you forgot your password, you can reset it through the 'password reset' option provided on the portal.

All GST taxpayers are required to use Multi-Factor Authentication (MFA) effective from 1st April 2025. In addition to username and password, MFA also asks for a second verification (OTP or Sandes App code). Make sure MFA is turned on, and if it is, be sure to use the extra authentication process if login is still failing after entering valid credentials.

2. Account Locked Due To Multiple Failed Attempts

Solution: Try again after some time (about 30 minutes) or reset your password with OTP.

An account lockout can also happen if the MFA verification process fails multiple times. Please make sure that your registered mobile numbers are active and receiving OTPs before attempting to log in.

3. Session Timeout

Solution: Log in again and do not idle a portal for more than 20 minutes.

Maintenance is scheduled generally on Sunday Nights (11 PM to 4 AM IST) on the GST portal, and occasional slowdowns are observed within 48-72 hours of the filing 
deadline. Make appropriate arrangements so that there are no interruptions during the session.

4. Page Not Loading Or Blank Screen

Solution: Delete the browsing history, disable all unnecessary browser extensions, and use a supported browser, such as Google Chrome or Edge.

For instance, if there is an IMS, QRMP, DRC-03, or e-invoicing update for the back end, then the corresponding sections in the portal might malfunction for a certain time, while the rest of the portal functions normally. If a particular section does not appear, wait one hour, delete the temporary files from the Web Browser, and try again.

5. OTP Not Received

Solution: Wait for 2 minutes, and ask for a new OTP. Ensure that your mobile phone number is not DND and is turned on.

The GST portal also supports the Sandes government app as an authenticator alternative to SMS OTP. If SMS OTPs are consistently delayed, switching to the Sandes app authenticator is now an officially supported option.

6. Invalid OTP Entered

Solution: Make certain that the OTP is used within 10 minutes of its generation. When it expires, ask for a new OTP.

If you request multiple OTPs consecutively, you'll be subjected to a 2-hour cooldown period before generating OTPs again. Please wait to try again; don't click ‘Resend OTP' multiple times within a short interval.

7. DSC Not Working On Portal

Solution: Re-register the DSC and ensure that the Embridge or eSigner utility is properly installed and running in the background.

GSTN requires only Class 3 DSCs for GST portal filing as of 2025. Ensure your DSC is a Class 3 certificate issued by an authorised Certifying Authority (CA) in India. 
Class 2 DSCs are no longer accepted on the portal.

8. EVC Option Not Available

Solution: EVC is generally available only for eligible taxpayers. If unavailable, use DSC for return filing.

EVC-based verification has an added layer. Taxpayers whose turnover exceeds thresholds eligible for DSC-only filing should ensure their authorised signatory's DSC is 
updated and registered on the portal.

GSTR-1 Filing Common Errors And Fixes

9. Invalid GSTIN Of The Recipient

Solution: Verify the GSTIN through the GST search portal before uploading invoices.

AI-backed back-end GSTIN validation tools have been introduced by GSTN, identifying wrong GSTINs while uploading GSTR-1. When a supplier's GSTIN is inactive, cancelled or invalid, GST invoices will be rejected and will not get uploaded to the buyer's GSTR-2B.

10. Invoice Number Exceeds 16 Characters

Solution: Edit the invoice number to ensure that it does not exceed 16 characters.

11. Duplicate Invoice Number

Solution: Make sure that no duplicate invoice numbers are used for the same tax period when submitting invoices.

12. Tax Amount Mismatch

Solution: If necessary, change the amount of taxes, making sure the values in the uploaded file are correct before the submission.

13. Place Of Supply Error

Solution: For B2B transactions, ensure that the place of supply corresponds with the recipient's state code.

GSTR-2B now separately flags ITC that is ineligible due to Place of Supply (POS) mismatches through the IMS framework. Taxpayers can conveniently track both eligible and ineligible ITC through the MYGST Refund CFO Dashboard, which provides clear visibility of claimable credits, POS-restricted credits, and other ITC reversals, helping ensure accurate reporting in GSTR-3B.

14. HSN or SAC Code Missing Or Invalid

Solution: Use the correct HSN or SAC code as required under GST regulations.

The 56th meeting of the GST Council in September 2025 and Budget 2026 have announced a restructuring of the GST rate slab with the reduction of two slabs with 12% and 28% rates and introduction of a new 40% slab for sin goods from April 1st, 2026. Check the updated slab structure in all your HSN codes and corresponding rates in your billing software.

15. Error Code RET00009

Solution: This usually means the return has already been submitted or filed. Check the return status instead of attempting a fresh filing.
Additionally, a portal error will occur if the portal tries to file a return for a period more than three years after it has been due.

16. JSON File Upload Failure

Solution: Meanwhile, try using the GST Offline Utility to validate and make sure that the file does not exceed the file size limit.

17. Invoice Amendment Rejected

Solution: Make sure that the amendment is submitted for the appropriate tax period and that the invoice information matches exactly.

18. E-Invoice Data Mismatch With GSTR-1

Solution: Do not manually modify IRN-linked invoices because they are auto-populated into GSTR-1. Get help from MYGSTRefund to identify E-Invoice data mismatches.

GSTR-3B Mismatch Issues And Fixes

19. ITC Mismatch With GSTR-2B

Solution: Reconcile your purchase register with GSTR-2B and claim only eligible matched credits.

20. Tax Liability Mismatch With GSTR-1

Solution: Review the values carefully before submission and ensure consistency across returns.

21. Negative ITC Balance Error

Solution: Check the electronic credit ledger and reduce the ITC claim accordingly.

22. Reverse Charge Liability Not Declared

Solution: Report applicable reverse charge liability in the appropriate section of GSTR-3B.

23. Wrong Tax Head Payment

Solution: Apply for rectification and use the appropriate process for re-credit where eligible.

24. Already Submitted Return Error

Solution: Make necessary adjustments in the next tax period through permissible correction mechanisms.

25. Interest Liability Not Auto-Calculated

Solution: Manually verify and calculate applicable interest on delayed tax payments.

26. Input Service Distributor ITC Missing

Solution: Claim the credit only after it appears in GSTR-2B.

27. Turnover Mismatch In Annual Return

Solution: Perform quarterly reconciliation between books, GSTR-1, and GSTR-3B. MYGSTRefund offers advanced GST reconciliation to help businesses maintain accurate GST records throughout the year.

System And Technical Errors

28. Undefined Error In The GST Portal

Solution: Clear cache, log in and log out, and raise a grievance if it persists.

29. System Error Occurred In The GST Portal

Solution: Wait another 15-30 minutes and repeat. Do not conduct filing when there is heavy traffic.

30. Gateway Timeout (502/504)

Solution: Try during off-hour periods (early morning and late evening).

31. PDF Generation Failure For The Acknowledgement

Solution: Wait for approximately 10 minutes and then use the download option again.

32. Digital Signature Error During Filing

Solution: Re-register the DSC and ensure it belongs to the authorised signatory registered on GSTN.

Only Class 3 DSCs are accepted on the GST portal. Ensure the DSC is registered against the correct PAN of the authorised signatory. The eMudhra emBridge utility or eSigner must be running as a background process during DSC-based filing

33. PAN Validation Failure

Solution: Verify that the PAN exactly matches the details linked to the GSTIN.

34. Bank Account Validation Error

Solution: Ensure the account is properly validated and updated for refund processing purposes.

35. Return Not Visible In Dashboard

Solution: Verify the selected financial year and tax period filters.

36. Challan Payment Not Reflecting in Ledger

Solution: Wait up to 20 hours. If this continues, complain with the 'CIN' reference number.

Registration And Amendment Errors

37. Aadhaar Authentication Failure During Registration

Solution: Make sure that the mobile phone is working with Aadhaar. If a problem still arises, use interchangeable verification documents as are permitted.

The use of biometric-based Aadhaar authentication for the new registration applicants of GST, with the introduction of a new system, has been made mandatory across the nation (GSTN Advisory, 12th February 2025).

If candidates do not choose to authenticate themselves by Aadhaar, then they should go to the designated GST Suvidha Kendra (GSK) for biometric verification and 
document verification. All Verifications must be completed within 15 days of Part B of REG 01; otherwise, the ARN will not be created.

38. Amendment Application Is Stuck In Processing

Solution: Monitor application status and escalate a grievance if no action is taken within 7 days.

39. Principal Place of Business Mismatch

Solution: Ensure that the address entered matches exactly with the uploaded utility bill or rental agreement.

40. Authorised Signatory Mobile Number Already In Use

Solution: Use a different mobile number because a single number cannot be used across multiple registrations in such cases.

41. GST Cancellation Application Rejected

Solution: Ensure all pending returns are filed and provide a valid cancellation reason before submitting the application.

How To Check Error Status On GST Portal

• Step 1: Log in to the GST portal.
• Step 2: Go to Services > Returns > Track Return Status.
• Step 3: Enter GSTIN & return Period.
• Step 4: Check the status column to see the error or filing status.
• Step 5: Submit a grievance for issues related to payment under Services > Payments > Grievance Against Payment.

MYGSTRefund helps your business stay GST-compliant with simple tools and technology. Use the MYGSTRefund platform for GST return filing, GST refund processing, GST litigation management, and a CFO dashboard with real-time insights—all in one place for easy and efficient GST management.

Conclusion

Navigating GST problems and solutions on the GST portal does not have to be stressful if you know what each error means and how to fix it. A solution to 'undefined 
error in the GST portal', 'GST portal system error, or an OTP failure is simple once you know the ‘why' and the ‘how'. File returns before the due date, use validated JSON files, keep your registered contact details updated, and use cloud-based GST return filing software to reduce errors at the source.

Frequently Asked Questions (FAQS)

1. What are some common errors in GST filing, and how can they be rectified? 
Incorrect GSTINs, duplicate invoices, inconsistent tax amounts, and unclear portal issues are typical mistakes. Most can be fixed by validating data before upload using the GSTN offline tool or cloud GST software.

2. How to check errors in the GST portal? 
Go to Services - Returns - Track Return Status on gst.gov.in. The portal shows the error description against the return filing attempt, along with an error code for further reference.

3. How to solve GST problems? 
Start by identifying the error code, checking the GSTN error description page, clearing your browser cache, and use validated JSON files. For persistent GST problems and solutions, raise a grievance on the portal.

4. What errors can occur during GST validation? 
Validation errors include invalid GSTIN format, HSN code not matching the commodity, invoice number exceeding 16 characters, tax rate mismatches, and place of supply errors that contradict the recipient's state.

5. What is error code RET00009 in GSTR-1? 
Error code RET00009 means the return for that period has already been submitted or filed. You cannot file again for the same period. Check your return status under Track Return Status to confirm the filing.