During filling & filing of GSTR 9C it was found that there is an error file generated by GSTN when Digitally Signed GSTR 9C is up-loaded and error is reflecting at PT III (9) at row Q & P – by saying “The amount paid by you mentioned at “Q” is not matching with amount reported by you in GSTR 9. Similar error reflected at “R” also.
After a long R & D it was found that amount of Tax paid as filled by assesse/CAs under Part III (9) – Q – Total amount paid as declared in Annual Return (GSTR 9) – is actually comparing by utility of GSTR 9C with the value filled in GSTR 9 – in Part IV Sr. No. 9 A, B & C and any adjustment in Part V Sr. No.10 & 11. (Please do not consider row 13 it is without RCM).
But what is important here when you fill PART III(9) of GSTR 9C then it asked to fill Interest, Late Fee, Penalty at L, M & N respectively but when it compares from GSTR 9 in Part IV it does not include Interest, Penalty etc. therefore an error arises while submitting 9C at portal.
Therefore, at the time of giving figures in GSTR 9C paid amount fill only IGST + CSGT + SGST + Cess if any and do not include late fee/penalty etc. so that your figure will be matched and form GSTR 9C will be processed.
Now, what will happen when you fill figures without Late fee etc. in Q a difference will arrive at R – as Un-reconciled payment (Q-P) equal to Penalty etc. this will be suitable answered in Part III (10) by Auditors –
Suggestive Language of Note: “The difference arises due to Interest, Late Fee, Penalty shown at Part III -9 l, M & N where Late Fee etc. is paid by client but in GSTR 9 Part IV Sr. No.9 A, B & C it is not included. The late fee has already been paid therefore no difference of Tax is payable.”
I hope this will help you. For any confusion you can revert to me.