Khan, who claims to be a scientist, had come out with a drug called 'Body Revival' which he claimed was a cure-all for a variety of diseases including the cancer.
According to him, Syed Wajid Hussain and Vilas Poddar demanded Rs eight crore from him, threatening to file false cases if he did not pay up.
Hearing a petition filed by Khan's son Munish, praying for transfer of investigation to an independent agency such as CID or CBI, the High Court today asked the Pune crime branch to probe the complaint.
Khan's firm Health Reactive manufactures and sells Unani and Ayurvedic medicines.
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He filed the complaint with Versova police here in April 2009. His petition said police registered the first information report only against Sayed Hussain, arrested him and filed a chargesheet.
The other accused got anticipatory bail, it said, adding that the investigation made no headway after that.
Transferring the probe to Pune police, the court disposed of the petition.
Khan himself was mired in a controversy when Food and Drugs Administration raided his premises here in 2008 and seized the drugs his company manufactured.