Kerala HC Allows GST Refund as Limitation Counted from date of payment under correct head

Pushpagiri Medical Society Vs State of Kerala (Kerala High Court)

The petitioner, a registered non-profit organization running a hospital and various medical education institutions in Kerala, is also a registered taxpayer under the Central Goods and Services Tax Act, 2017 (CGST Act) and the Kerala Goods and Services Tax Act, 2017. The writ petition concerns the rejection of refund applications filed by the petitioner for amounts mistakenly paid toward the Kerala Flood Cess.

The Kerala Flood Cess was introduced by the State Government through the Finance Act, 2019, with effect from June 2019, to address the crisis caused by the floods in Kerala in 2018. Due to confusion regarding the procedure for payment of the Cess for the period from August 2019 to July 2021, the petitioner remitted the amounts through GSTR Form-1 instead of through Form KFC-A, which was the correct mode of payment.

Since the payments were not credited under the correct account, proceedings were initiated against the petitioner, informing it that payment toward the Cess had not been properly made for the relevant period. Upon receiving the notice, the petitioner realized the mistake and made the correct payment on 10.03.2025. Certificates evidencing such payment were issued by the State Tax Officer on 28.07.2025.