In a filing to the stock exchanges today, the airline said last month the regulator sought views of the statutory auditors and the audit committee on certain allegations.
However, the carrier did not elaborate on the complaint.
Referring to the reports, the airline said similar allegations had earlier been communicated to it by Sebi in June 2016, based on a complaint received by the regulator.
"The company had provided its response to Sebi in July 2016. No further communication was then received from Sebi in the matter," the filing said.
Further, the airline said that in a communication on April 30, 2018, Sebi forwarded to the company "another complaint received by it" containing substantially similar allegations.
The regulator also sought the views/recommendations of the statutory auditors and the audit committee of the company on the same, it added.
"The company has already taken necessary steps in this regard as directed by Sebi and is in communication with Sebi in the matter," the filing said.
There was no immediate response from a Jet Airways spokesperson on the issue.
After posting a Rs 10.36 billion loss in the three months ended March 2018 mainly due to high oil prices and a weaker rupee, Jet Airways last week said that it may see a rise in debt for the next one or two quarters.
Shares of Jet Airways rose nearly 2 per cent to Rs 427.30 in late morning trade on the BSE.
Earlier this week, rating agency Icra lowered its credit ratings on Jet Airways' short-term and long-term loan facilities citing weakened financial performance as the airline is unable to pass on rise in jet fuel prices to the customers.