A central govt. company has deducted Late delivery charges including GST tax against material late supply and issue an invoice. ITC is reflecting in our GSTR 2A, can we take this ITC?

Reply—As per Section 15 of CGST Act, the value of supply shall include interest or late fee or penalty for delayed payment of any consideration for any supply. But in your case the recipient of goods has charged late supply charges from the supplier. It is neither supply of goods nor supply of service. It is actually deduction made from your supply bill and it is to be treated as debit note issued by him. Since it is not restricted under section 17(5) of CGST Act, ITC can be claimed.