The Karnataka government had transferred the case to the agency last month.
"After taking over the case, CBI has formed a 12-Member Multi-Disciplinary Investigation Team (MDIT) comprising of its investigators who are being assisted by Chartered Accountants, Forensic Auditor, Computer Forensic Experts, and Bankers," the CBI said in a statement.
Khan's firm has been accused of duping thousands of people by promising high returns using Islamic ways of investment.
The scam came to light in June this year after the prime accused, Khan, fled the country, leaving behind an audio message, in which he threatened to commit suicide due to alleged 'harassment' by some politicians and goons.
Khan was arrested in July on his arrival from Dubai after a Special Investigation Team (SIT) probing the scam located and persuaded him to come to India and submit before the law. Following this, he was sent to the judicial custody.