Penalty for not auditing the books of accounts of a company

What type of Audit are your talking about - Statutory Audit, Income Tax Audit or GST Audit ???

Incase of failure of GST Audit, then the Penalty will be as follows :

GENERAL PENALTY of Rs. 50,000 ( Rs. 25k under CGST + Rs. 25k under SGST ) under Section 125 of the CGST Act 2017 can be levied on the company on failure to conduct GST Audit under Section 35(5) of the CGST Act 2017 read with Rule 80(3) of the CGST Rules 2017.