Interest under Section 50 of the CGST Act is compensatory in nature and can be levied only on the portion of tax actually paid in cash, since tax discharged through ITC does not result in any loss of revenue to the Government.
Section 50(1), after amendment by the Finance Act, 2019 (retrospectively effective from 01.07.2017 vide Notification No. 16/2021-CT dated 01.06.2021), specifically provides that interest shall be payable only on that portion of tax paid by debiting the electronic cash ledger, except in cases covered under Section 73(11) or Section 74.
The provision does not restrict its applicability only to delayed filing of GSTR-3B returns. The language used is "tax unpaid or paid belatedly". Therefore, wherever tax liability is ultimately discharged partly through ITC and partly through cash, interest can arise only on the net cash liability.
Audit findings merely determine short payment or non-payment of tax. Once such liability is discharged through available ITC, the portion adjusted through ITC cannot be treated as revenue withheld from the Government. Hence, levy of interest on the gross liability defeats the legislative intent behind the retrospective amendment.
This position also stands supported by judicial precedents.
Further, CBIC itself, through its press release dated 26.08.2020 and subsequent amendment, acknowledged the legislative intent that interest is to be levied only on net cash tax liability.
Therefore, the departmental contention that net liability principle applies only to GSTR-3B filings and not to audit demands is legally unsustainable, unless the case falls under Section 73(11) or Section 74 involving fraud, suppression, or detention of tax beyond prescribed situations.