GST WEEKLY UPDATE :11/2025-26 (15.06.2025) By CA Vipul Khandhar

-By CA Vipul Khandhar

1. System Validation for Filing of Refund Applications on GST Portal for QRMP Taxpayers:

1. In the month of 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. As per the said circular:

“Any refund claim for a tax period may be filed only after furnishing all the returns in FORM GSTR-1 and FORM GSTR-3B which were due to be furnished on or before the date on which the refund application is being filed. However, in case of a claim for refund filed by a composition taxpayer, a non-resident taxable person, or an Input Service Distributor (ISD), furnishing of returns in FORM GSTR-1 and FORM GSTR-3B is not required. Instead, the applicant should have furnished returns in FORM GSTR-4 (along with FORM GST CMP-08), FORM GSTR-5 or FORM GSTR-6, as the case may be, which were due to be furnished on or before the date on which the refund application is being filed.”

2. 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.

3. Post implementation of the above validation, it was observed that taxpayers registered under the Quarterly Return Monthly Payment (QRMP) scheme encountered issues while attempting to file refund applications. Specifically, the 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.

4. This is to inform the taxpayers that the aforementioned technical issue has now been resolved. Taxpayers under the QRMP scheme can now file refund applications for the invoices for which GSTR-3B has been already filed. Please note 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.

5. All taxpayers are advised to ensure that relevant returns are filed prior to filing a refund application, as per the legal provisions and existing system validations.

6. In case of any discrepancies or system-related queries, taxpayers may reach out to the GST Helpdesk (https://selfservice.gstsystem.in) 

2. Advisory on filing of Amnesty applications under Section 128A of the CGST Act:

• As on 08.06.2025, a total of 3,02,658 waiver applications have been filed through SPL-01/02. However, it has come to notice that certain taxpayers are facing difficulties in filing amnesty applications under Section 128A on the GST portal. In view of the approaching last date for submission, various trade bodies have submitted representations requesting an alternate mechanism to facilitate filing.
• In view of the above, taxpayers who are facing technical issue which is restricting them to file waiver application are advised to adopt the steps outlined in the below link:

https://tutorial.gst.gov.in/downloads/news/link_data.pdf

• Difficult if any, faced by the taxpayers in filing applications through this route may immediately be brought into the notice of GSTN by raising a complaint on GST Self-service portal : (https://selfservice.gstsystem.in)

3. Filing of SPL-01/ SPL-02 where payment made through GSTR 3B and other cases:

While filing amnesty applications in Form SPL-01 or SPL-02 under Section 128A of the CGST Act, 2017, some taxpayers are facing technical issues related to auto population of payment details in Table 4 of the forms.

In particular, it has been observed that in certain instances, 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 the above cases, taxpayers are 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.

In all such cases, it is advised to upload the relevant payment information as attachments along with the online application for the verification by the jurisdictional officer.

4. Delhi GST Department has issued Guidelines for Mandatory Conduct of Personal Hearings through Virtual Mode in All Proceedings (vide Circular No. F.3(640)/GST/P&R/2025/348-55 dated June 13, 2025):

Accordingly, to ensure transparency, efficiency, and strict adherence to the principles of natural justice, the following guidelines are being issued to outline the procedures and protocols to be followed during virtual hearings. All Proper Officers, including Appellate Authorities—hereinafter referred to as “the Authority”—appointed and functioning under the provisions of the Delhi GST Act, 2017 and the Rules framed there under, are hereby directed to comply with the following guidelines:

1. In any proceeding, all the personal hearings shall mandatorily be conducted in virtual mode and no person shall be required to appear in person for personal hearing.
2. Such virtual hearings shall be conducted through available applications such as WEBEX, Google-Meet etc. The date and time of hearing along with a link for the virtual hearing shall be informed well in advance to the taxpayer or authorized representative through the registered email id and/or mobile number.
3. In the said e-mail, Authority shall also provide details of the staff/officer who would provide assistance to the party, for conducting the virtual hearing. This link shall not be shared with any other person without the consent of the said officer.
4. The taxpayer or his authorized representative shall download the required application on their computer system/laptop/mobile phone beforehand and be ready with appropriate network connectivity and bandwidth for the virtual hearing and join the same at the time and date allocated to them.
5. The taxpayer or authorized representative shall be required to submit his vakalatnama or authorization letter along with the copy of his photo-id card and provide contact details well in advance to the said officer, devoid of which he shall not be allowed to represent the taxpayer.
6. The virtual hearings shall be conducted from office of the concerned Authority only.
7. All persons participating in the virtual hearing shall be appropriately dressed and shall maintain the decorum and dignity at all times.
8. The submissions made by the taxpayer or his authorized representative during the virtual hearing shall be recorded as “Record of Personal Hearing” by the concerned Authority on online PM module and after generating it in pdf format, Authority shall put his signature and share thereon. A copy of such saved “Record of Personal Hearing” shall be shared on the registered e-mail id of the taxpayer. Additionally, it shall also be sent on the e-mail id provided by the taxpayer or his authorized representative in Para e hereabove.
9. In case of any adjournment, a notice of adjournment shall also be sent through BO Portal mentioning details of next date of hearing.
10. If the taxpayer/authorized representative prefer the Authority to consider any document including additional documents during the virtual hearing, he may do so by sending the scanned copy of such self-attested document via official mail to the Authority concerned before virtual hearing.
11. In cases of requirement of submission of physical set of documents the same shall be submitted after due attestation by the taxpayers or his authorized representative, to the Authority concerned during working hours.

The proceedings of virtual hearing as well as documents submitted in the above manner shall be deemed to be valid document/record for the purpose of the CGST/DGST Act and Rules made there under read with section 4 of the Information Technology Act, 2000.

It is made clear that while conduct of personal hearing through virtual mode is being made mandatory, there may yet be rare and extenuating circumstances on the part of the taxpayer or his authorized representative on account of which this cannot be done. Each such request shall be approved only by the Zonal In-charge/officer concerned after recording the reasons for the same.

5. Important Judgements:

(i) The Hon’ble Sikkim High Court Decision Regarding refund of unutilized Input Tax Credit (“ITC”) can be claimed even in case of closure of business:

(Applicant – SICPA India Private Limited)

The Court observed that there is no express prohibition under Section 49(6) read with Sections 54 and 54(3) of the Central Goods and Services Tax Act, 2017 (“the CGST Act”) restricting such refund. Although Section 54(3) of the CGST Act prescribes specific scenarios where refund is generally permitted, the Court emphasized that the statute does not authorize retention of tax without legal backing, thereby supporting the entitlement to refund in such cases.

Disclaimer:

This publication contains information for general guidance only. It is not intended to address the circumstances of any particular individual or entity. Although the best of endeavour has been made to provide the provisions in a simpler and accurate form, there is no substitute to detailed research with regard to the specific situation of a particular individual or entity. We do not accept any responsibility for loss incurred by any person for acting or refraining to act as a result of any matter in this publication.

(Author is a well known Chartered Accountant practicing in the field of Direct and Indirect taxes at Ahmedabad)