"We filed the charge sheet on Tuesday before the special Prevention of Money Laundering Act (PMLA) court, said an ED official.
The charge sheet also names Khan's wife Ruksana and sons Munish and Sarosh; all of them booked under the PMLA Act.
The ED recently attached Khan's properties.
Khan, arrested in May 2010 (later he got bail) is accused of cheating over 120 people by claiming that his medicine 'Body Revival' can cure all diseases including cancer and he had some celebrity clients. The medicine was priced at Rs 16,000 for a 100 ml bottle.
In 2009, Khan's clinic at suburban Versova was raided by the Food and Drugs Administration. He was also booked under relevant sections of Indian Penal Code, Drugs and Magic Remedies (Objectionable Advertisements) Act and Maharashtra Medical Practitioners Act.