Common portal of GST under the GST law, GSTN keeps on issuing advisories on new functions / updates on the portal for upgradation of functionalities and new options or functions enabled for implementation by taxpayers.
During the month of June, 2025, the following advisories have been issued so far in relation to the various compliances by GSTN:
- GSTN Advisory on barring of GST Returns on expiry of three years
- GSTN Advisory on non-editability of auto-populated liability in GSTR-3B
- Advisory on Refund applications for QRMP Taxpayers
- GSTN Advisory on filing of application under Amnesty Scheme
- Advisory on filing of Forms for Amnesty Scheme
- Introduction of enhanced Inter-operable Services between E-Way Bill Portals
- Filing of pending returns before expiry of 3 years
The gist of these advisories is summarized below:
GSTN Advisory on barring of GST Returns on expiry of three years
- W.e.f. 01.10.2023 (vide Notification No. 28/2023-CT dated 31.07.2023), taxpayers are not allowed file their GST returns after the expiry of a period of three years from the due date of furnishing the said return under Section 37 ( Outward Supply), Section 39 (payment of liability), Section 44 (Annual Return) and Section 52 (Tax Collected at Source).
- These Sections cover returns, viz, GSTR-1, GSTR 3B, GSTR-4, GSTR-5, GSTR-5A, GSTR-6, GSTR 7, GSTR 8 and GSTR 9.
- GSTN has therefore, advised that there returns shall be barred for filing after expiry of three years. The said restriction will be implemented on the GST portal from July 2025 tax period. Taxpayers will no longer be allowed to file GST returns after the expiry of three years from their original due date.
- Thus, taxpayers have been advised to reconcile their records and file their GST Returns as soon as possible, if not filed till now.
(Source: GSTN Advisory dated 07.06.2025 read with Advisory dated 29.10.2024)
GSTN Advisory on non-editability of auto-populated liability in GSTR-3B
- GSTN has issued an advisory relating to auto-populated liability in GSTR-3B to be made non-editable.
- GST Portal provides a pre-filled GSTR-3B, where the tax liability gets auto-populated based on the outward supplies declared in GSTR-1/ GSTR-1A/ IFF. As of now taxpayers can edit such auto populated values in form GSTR 3B itself.
- With introduction of form GSTR 1A, taxpayer now has a facility to amend their incorrectly declared outward supplies in GSTR-1/IFF through GSTR-1A, allowing them an opportunity to correct their liabilities before filing their GSTR-3B in the same return period.
- Therefore, w.e.f. July, 2025 tax period for which form GSTR 3B will be furnished in August, 2025, such auto-populated liability will become non-editable.
- Therefore, taxpayer have been advised that they will be allowed to amend their auto populated liability by making amendments through form GSTR 1A which can be filed for the same tax period before filing of GSTR 3B.
(Source: GSTN Advisory dated 07.06.2025 read with advisories dated 27.01.2025 and 17.10.2024)
Advisory on Refund applications for QRMP Taxpayers
- GSTN has issued Advisory on System Validation for Filing of Refund Applications on GST Portal for QRMP taxpayers.
- In May, 2025, a system-level validation was deployed on the GST Portal to ensure adherence to the provisions outlined in Para 6 of Circular No. 125/44/2019-GST dated 18.11.2019.
- Accordingly, the GST system was updated to allow refund applications only if the taxpayer had filed all relevant returns that were due up to the date of filing the refund application.
- However, taxpayers under QRMP Scheme experienced that system was not recognizing invoices furnished using the Invoice Furnishing Facility (IFF) for the first two months of the quarter (M1 and M2), resulting in the inability to proceed with refund filing. Additionally, in cases where GSTR-1 for the previous quarter had already been filed, the system was erroneously prompting taxpayers to file returns for M1 and M2 of the current quarter too. Taxpayers were facing this issue when the refund application was being submitted during the period between the two quarters.
- GSTN has now advised that taxpayers under the QRMP scheme can now file refund applications for the invoices for which GSTR-3B has been already filed, but invoices furnished through IFF for which GSTR-3B is yet to be filed in coming return period should not be included in the refund application.
- GSTN has further the advised to ensure that relevant returns are filed prior to filing a refund application, as per the legal provisions and existing system validations.
(Source: GSTN Advisory dated 10.06.2025)
GSTN Advisory on filing of application under Amnesty Scheme
- GSTN has issued an Advisory on filing of Amnesty applications under Section 128A of the CGST Act, 2017 for taxpayers filing difficulties in filing applications on the GST common portal. Accordingly,
- GSTN has received 3,02,658 waiver applications as on 08.06.2025.
- GSTN has been represented that certain taxpayers are facing difficulties in filing amnesty applications under Section 128A on the GST portal.
- Taxpayers who are facing technical issue which is restricting them to file waiver application are advised to adopt the following steps.
- Taxpayers may adopt the alternative route of manual entry of order details on the portal, viz,
√ While initiating the filing of application, taxpayers are advised to enter ‘No’ against ‘Whether the demand order is issued through the GST Portal’
√ In the field “Details of demand order”, taxpayers shall enter the order number with the prefix of “ONL”.
√ The editable details in the Basic Details table shall be entered manually
√ Once this step is completed, the Order details, Payment details, and Demand related information can be entered manually by the taxpayer.
√ In cases where the taxpayer has made the duty payment through DRC-03, the relevant details may be furnished in Table 4. However, if the payment has been made using the ‘Payment towards demand’ option, such details cannot be entered in this table. Taxpayers are accordingly advised to upload the payment details separately in such cases.
(Source: GSTN Advisory dated 11.06.2025)
Advisory on filing of Forms for Amnesty Scheme
- GSTN has issued an advisory for filing of SPL-01 and SPL-02 where payment made through GSTR 3B and other cases in relation to auto-population of payment details in Table 4 of the forms.
- In some cases, the payments details may not be accurately auto-populated in the applications filed by the taxpayers:
(a) Amount paid through “payment towards demand order” functionality
(b) Pre-deposit amount details
(c) Payment made through GSTR 3B
- In such cases, taxpayers have been advised to proceed with filing of waiver application as GST portal doesn’t stop the taxpayers from filing the application in case wherever the payment details and demand amount are not matching.
- It is also advised to upload the relevant payment information as attachments along with the online application for the verification by the jurisdictional officer.
(Source: GSTN Advisory dated 12.06.2025)
Introduction of enhanced Inter-operable Services between E-Way Bill Portals
- GSTN has advised that NIC shall be introducing enhanced inter-operable services between E-way bill portals with launch of new e-way bill 2.0 (https://ewaybillgst.gov.in)e.f. 1st July, 2025.
- It will provide enhanced inter-operability between the existing E-Way Bill 1.0 Portal (https://ewaybillgst.gov.in) and the new portal. It enables cross-portal access to critical E-Way Bill functionalities, ensuring seamless operations for taxpayers and transporters.
- The following additional services will be available on the E-Way Bill 2.0 portal for E-Way Bills generated on either portal (E-Way Bill 1.0 or E-Way Bill 2.0):
a) Generation of E-Way Bill based on Part-A details entered by the supplier
b) Generation of Consolidated E-Way Bills
c) Extension of validity of E-Way Bills
d) Update of transporter details
e) Retrieval of consolidated E-Way Bills
- Both portals will operate on a real-time synchronised architecture wherein E-Way Bill data will be mirrored across both systems within seconds. This dual-system approach is designed to eliminate dependency on a single portal and ensure business continuity.
- Services will also be made available to taxpayers and logistics operators through APIs, in addition to the web portal interface. These APIs are currently hosted on the sandbox environment for testing and integration purposes.
- Eventually, the data from both E-Way Bill1 and E-Way Bill2 portals shall be seamlessly merged and integrated, thereby eliminating dependency on the E-Way Bill1 system during exigencies.
- Criss-cross operations between the two portals are fully enabled updates made to E-Way Bills generated on the E-Way Bill1 portal can be carried out on the E-Way Bill2 portal, and vice versa.
- In the event of non-availability of the main portal due to technical reasons, Part-B details of E-Way Bills generated on the E-Way Bill1 portal can be updated through the E-Way Bill2 portal, and both versions of the E-Way Bill slip may be carried accordingly.
(Source: GSTN Advisory dated 16.06.2025)
Filing of pending returns before expiry of 3 years
- GSTN has issued an advisory for filing pending returns before expiry of three years.
- As per Notification No. 28/2023-CT dated 31.07.2023, w.e.f. 01.10.2023, the taxpayers shall not be allowed file their GST returns after the expiry of a period of three years from the due date of furnishing the said return under Section 37 (outward supply), Section 39 (payment of liability), Section 44 (annual return) and Section 52 (Tax Collected at Source). These sections cover GSTR-1, GSR-1A, GSTR 3B, GSTR-4, GSTR-5, GSTR-5A, GSTR-6, GSTR 7, GSTR 8 and GSTR 9 or 9C.
- These returns will be barred for filing after expiry of three years.
- This restriction will be implemented on the GST portal from July, 2025 tax period.
- Accordingly, any return for which due date was three years back or more and hasn’t been filed till July Tax period will be barred from Filling. In this regard an advisory was already issued by GSTN on October 29th, 2024.
- Therefore, GSTN has advised the taxpayers to reconcile their records and file their GST Returns as soon as possible if not filed till now.
(Source: GSTN Advisory dated 18.06.2025)
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