The full service airline is grappling with financial woes and is looking to raise funds.
"As per the directions of State Bank of India, a forensic audit of specific transactions of the company for the period April 1, 2014 to March 31, 2018 is in progress.
"The company is fully cooperating with the auditors and providing them all the information, as is being sought in this connection," Jet Airways said in a regulatory filing.
The airline has been in the red for three consecutive quarters.
Sources had said the audit was ordered following a complaint of alleged financial irregularities in Jet Airways accounts by a whistleblower.
In August, the government had ordered an inspection of books and papers of the airline.
Last month, chief executive officer Vinay Dube said the airline was in active discussions with various investors to secure sustainable financing.