"The I-T department is looking into the payments made by NSEL to FTIL to see the money trail and verify sources of funds transferred by the exchange to its promoter," a finance ministry official said.
NSEL did not immediately offer any comment.
According to the balance sheet of the National Spot Exchange Ltd (NSEL), 'business support charges' paid to FTIL more than doubled to Rs 33.8 crore in 2012-13 from Rs 15.56 crore in 2011-12. NSEL pays business support charges to FTIL for using its trading platform.
NSEL, part of the Jignesh Shah-led Financial Technologies group, is grappling with a payment crisis as it settles Rs 5,600 crore of dues after suspending trading on July 31 following a government directive.
Besides, the I-T department is seeking information from top eight brokers who had an exposure of over Rs 50 crore in NSEL's commodity futures trading.
"We are verifying the source of investor money. We are seeking information from top eight brokers to find out who are the ultimate beneficiaries," the official added.
There are around 17,000 investors in NSEL, out of which 9,000 traded through the top eight brokers, including Anand Rathi, Motilal Oswal, India Infoline and Systematix.
The I-T department's probe is in addition to one by the Enforcement Directorate, which has reportedly found violations of Foreign Exchange Management Act (Fema) norms.
FTIL shares plummeted 10.25 per cent to Rs 150.20 at the close on the BSE today.
FTIL's statutory auditor Deloitte Haskins & Sells yesterday withdrew its report certifying the company's accounts for fiscal 2012-13, saying it cannot be "relied upon" any "longer" in the wake of the payment crisis at the firm's subsidiary NSEL.
NSEL has defaulted on six consecutive weekly payments to be made to its investors.
FTIL has maintained that the impact of NSEL on the company is not 'material' in the standalone financial statement as the contribution of the bourse's revenue in the company's net profit is only 6.56 per cent.
A high-level panel headed by Economic Affairs Secretary Arvind Mayaram has submitted a report on NSEL to Finance Minister P Chidambaram and the Prime Minister's office. The report has brought to light minor systemic failures in the functioning of the commodity exchange.