The other man accused in the case is Sachin Waze, former Assistant Police Inspector in the Crime Intelligence Unit (CIU).
The "fake encounter" was initially planned in the Maruti Eeco vehicle, which was stolen from Maharashtra's Aurangabad city in November last year.
Deshmukh resigned as Maharashtra's home minister on Monday after the HC directed Central Bureau of Investigation (CBI) probe.
It directed the Central Bureau of Investigation's (CBI) director to complete the preliminary inquiry within 15 days and then take a decision on further course of action.
There should be a probe against Anil Deshmukh as he is under suspicion at this moment, Athawale said.
Anil Deshmukh had on Saturday refuted all the allegations against him said that he is filing a defamation suit against the former Mumbai Police Commissioner.
Waze, arrested for his alleged role in the Mukesh Ambani bomb scare case on March 13, was attached to the Crime Intelligence Unit (CIU) of Mumbai police's crime branch till recently.
The National Investigation Agency (NIA) arrested Waze on late Saturday night in connection with its probe into the recovery of a Scorpio containing 20 gelatin sticks near Ambani's house.
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