Both are believed to be outside India.
District Judge H M Patwardhan issued the warrants today.
Thane police raided Avon Lifesciences in Solapur last year and seized around 18.5 tonne of ephedrine worth Rs 2,000 crore.
As per the police, ephedrine was being diverted from Avon Lifesciences to a Kenya-based drug cartel headed by Goswami where it was used to make party-drug Methamphetamine.
The police have arrested more than 10 persons in the case.