Role of chartered accountant or a cost accountant in certifying reconciliation statement: There are apprehensions that the chartered accountant or cost accountant may go beyond the books of account in their recommendations under FORM GSTR-9C. The GST Act is clear in this regard. With respect to the reconciliation statement, their role is limited to reconciling the values declared in annual return (FORM GSTR-9) with the audited annual accounts of the taxpayer. This was the clarification issued by CBIC on 04-07-2019.
Inference: If an auditor has to go by this, he just has to tally the amount stated in books and GSTR 9. He doesn't have to check if Input is availed only on eligible items, he doesn't have to check if wrong rates of tax has been charged on outward supplies, he doesn't have to check if there is any reversal in ITC needs to be done and many more... On the whole the GST Auditor need not do an AUDIT... Just a mere reconciliation of books with GSTR 9.
What can be done: GSTR - 9 requires more information than GSTR - 9C. And the government asks the taxpayer himself to prepare GSTR - 9. And going by the above clarification auditor doesn't have to check the information provided in GSTR 9. He just has to tally the books and GSTR 9. I believe that both GSTR 9 and GSTR 9C should be merged into one single form and that form should be certified by a GST Auditor. This would be much effective and it would serve the purpose.
The views expressed are just my personal opinion.