Since GSTR 2 not yet available whose intention was also to report ITC which is not yet reflecting and looking at its intention primafacie it seems that later on government will give credits for such bills available with you but credit not yet reflecting.
You will have to reverse the credit taken with respect to the bills for which the supplier have not filed/ shown in GSTR-1 (it can be verified by reconciling with GSTR-2A). Also you will have to pay the interest for the said credit. Further you will have to show in table 12 in GSTR-9 as ITC reversed avialed in previous year.
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