The shares of Mr Khan's co-owned T20 cricket team, Kolkata Knight Riders or KKR, had allegedly been undervalued, which led to a loss of foreign exchange to the extent of Rs 73.6 crore.
The agency had earlier issued a show-cause notice to Mr Khan and his wife Gauri, actor-friend Juhi Chawla and others. Ms Chawla and her husband Jay Mehta are also part owners of the team.
But Mr Khan had not appeared before the agency. In 2011, he was quizzed for allegations that KKR had received illegal money transferred from certain foreign tax havens.