One of my client had wrongly paid CGST and SGST instead of IGST on his outward supplies which was identified at the time of filing GSTR-9. What action to be taken now by the auditor while filing GSTR-  9C? Is there any relief given by the department in these types of cases. if so kindly share the same with reference to such notification.

Reply—

As per section 77 of CGST Act, A registered person who has paid the Central tax and State tax or, as the case may be, the central tax and the Union territory tax on a transaction considered by him to be an intra-State supply, but which is subsequently held to be an inter-State supply, shall be refunded the amount of taxes so paid in such manner and subject to such conditions as may be prescribed.

And as per section 19(2) of IGST Act, a registered person who has paid central tax and State tax or Union territory tax, as the case may be, on a transaction considered by him to be an intra-State supply, but which is subsequently held to be an inter-State supply, shall not be required to pay any interest on the amount of integrated tax payable.

So in  this case taxpayer need to pay the taxes in correct head without interest and can claim refund of taxes paid earlier under wrong head.