By mistake I paid cgst and sgst on inter state sales in the month of sep 17. I have also filed gstr 1 for sep 17 showing liability of igst. What can I do now to rectify the payments made under wrong heads? Will I be required to pay any interest/penalty on this wrong payment?
IGST would be matched with state and center so there is nothing to worry. But the problem here is that IGST will be shared with state to which you supplied.
In your case you paid SGST so that money will be going to account of your local state. The actual state where your supply is consumed will lose tax.
In your March GSTR-3B, reverse CGST and SGST and show liability under IGST. That will solve the matter. Interest is not required as you have already paid tax though in wrong head.
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