Statutory IGST Refund Cannot Be Denied Due to Web Portal

Statutory IGST Refund Cannot Be Denied Due to Web Portal Glitches and Must Be Processed Manually

Issue

Whether an IGST refund claim statutorily recognized under Section 54 of the CGST/TNGST Act can be denied or refused manual processing due to technical errors and system mismatches on the web portal.

Facts

Refund Application: The petitioner filed online IGST refund claims under Section 54 in respect of four shipping bills.
Portal Glitches Encountered:
- For three shipping bills, the portal threw an error indicating that the “Eligible latest scroll amount” did not tally with the “Sum of eligible latest GST amount.”
- For one shipping bill, the system incorrectly indicated “Scroll already generated” showing IGST as already sanctioned.
Rejection of Manual Processing: The respondent passed an order refusing to process the refund claims manually, citing portal errors and the absence of a manual mechanism.
Writ Challenge: The petitioner filed a writ petition challenging the rejection order and seeking directions for manual processing of the refund claims.

Decision

Statutory Rights Over System Glitches: A statutorily recognized IGST refund claim under Section 54 cannot be denied or curtailed merely due to technical glitches or system errors on the web portal [Para 2].
Duty to Process Refunds: Revenue authorities are duty-bound to process and grant valid refund amounts in accordance with the law despite technical impediments [Para 2].
Order Quashed for Manual Processing: The impugned rejection order was quashed, and the respondent was directed to accept physical documents and process the petitioner’s refund claims manually [Paras 2, 3].
Outcome: Decided in favour of the assessee by way of remand for manual processing [Paras 2, 3].

Key Takeaways

Primacy of Substantive Law: Administrative or portal limitations cannot override substantive statutory rights to tax refunds under GST law.
Obligation for Manual Intervention: When automated processing fails due to system scroll mismatches or portal errors, tax authorities must process claims manually upon submission of physical documentation.
Protection Against Technical Defaults: Taxpayers cannot be made to suffer or forfeit legitimate claims due to technical or software glitches in government web portals.

HIGH COURT OF MADRAS

Vishwanath Industries Infra Solutions (P.) Ltd.

Assistant Commissioner of Customs

C.Saravanan, J.

W.P. (MD) No.4849 of 2026

JULY 14, 2026

G.Natarajan for the Petitioner. R.Gowri Shankar, Senior Standing Counsel for the Respondent.

ORDER

1. The petitioner is before this Court challenging the impugned order dated 10.12.2025, whereby the request of the petitioner to process the online refund claims filed by the petitioner for refund of IGST under the provisions of the respective GST enactments has been rejected with the following observations:

“2. It is intimated that IGST Refund is complete automated system driven process. In other words, once you file GST returns, the data from GSTN will automatically be transmitted to the Customs System (ICES) and upon found being matched with the date of ICES, the system automatically sanction IGST refund. On verification of the 4 Shipping Bills on ICES system, the following errors populated, as mentioned below;

Sl No	SB No	SB Date	IGST Refund Error Status (Screenshot of message appearing enclosed)
1	7642106	08.02.2023	Eligible latest scroll amount does not tally with sum of eligible latest GST amount.
2	6680120	04.01.2023	Eligible latest scroll amount does not tally with sum of eligible latest GST amount.
3	7867231	17.02.2023	Eligible latest scroll amount does not tally with sum of eligible latest GST amount.
4	7229669	24.01.2023	Scroll is already generated. Scroll No.60262/2024 dated 25.11.2024. IGST Amt sanctioned is Rs.469637/-

3. It is further informed that there is no legal as well as practical provisions available at out end to sanction IGST manually. This is for your kind information please.”

2. On a perusal of the impugned order, I am of the view that it is unsustainable, as the benefit of refund claims, which is statutorily recognised under the provisions of the respective GST Enactments, cannot be curtailed or denied merely on account of technical issues arising in the web portal. The respondent is duty-bound to refund the amounts in accordance with the provisions of the respective GST Enactments, 2017. Therefore, the impugned order is quashed.

3. Therefore, I quash the impugned order and direct the respondent to process the refund claims of the petitioner manually by accepting the requisite documents in physical form and pass appropriate refund orders, as expeditiously as possible, preferably within a period of six weeks from the date of receipt of a copy of this order.

4. Accordingly, this Writ Petition stands disposed of. There shall be no order as to costs.