A reluctant Srinivasan had to be forced by the court to step aside nearly three weeks ago, until the BCCI completed an investigation into corruption in the Indian Premier League.
"Having come to know the nature of the allegations, we cannot close our eyes," the court said in a statement according to the Press Trust of India. "All these allegations were brought to his (Srinivasan's) notice but he did not take any action. That means he was aware about the allegations and did not take them seriously."
The court also asked the BCCI to share plans of its investigation during a hearing next Tuesday.
Srinivasan's position as BCCI chief became untenable when a three-member committee headed by Justice Mukul Mudgal found Gurunath Meiyappan, principal of IPL team Chennai Super Kings, guilty of being in contact with illegal bookmakers in a report to the Supreme Court.
Meiyappan, Srinivasan's son-in-law, was indicted in February.
Srinivasan is the managing director of India Cements, the company that owns Chennai Super Kings.
He is also due to become the International Cricket Council chairman in July.
The court appointed test great Sunil Gavaskar as interim BCCI president for the duration of the IPL, which was due to begin late Wednesday.