Customs must process IGST refund on exports covered by manual shipping bill; refund cannot be denied by shifting jurisdiction to GST Department: Madras High Court

The Court held that Rule 96(3) places processing of IGST refunds on exported goods with the Customs system or proper officer of Customs, ending a jurisdictional deadlock between the two departments.

The Madras High Court has directed the Customs Department to process and sanction, with interest, the IGST refund on exports covered by Manual Shipping Bill No. 117972 dated 14.03.2019, within four weeks [M/s TD Power Systems Ltd v. Commissioner of Customs & Ors].

Justice Hemant Chandangoudar noted that the exporter shipped AC generators worth Rs. 10.16 crore under a shipping bill whose Let Export Order could not be registered due to an ICEGATE technical issue. Customs accepted the export through a manual Let Export Order and later regularised it by a manual shipping bill.

Customs closed the refund request saying it fell within the GST Department's jurisdiction, while the GST Department stated that it had no jurisdiction under Section 54 to sanction IGST refunds on exported goods. The Court held that Rule 96(3) assigns processing to the Customs system or proper officer of Customs once a valid GSTR-3B is furnished, and Customs could not reject the claim on jurisdiction.

2026-juristway.com-2987-HC(Madras)-GST  |  High Court of Madras  |   30.09.2026