The FIR was registered yesterday against Darekar and others, including former chairman of the bank Shivaji Nalawade, officer Prakash Shirwadkar, on a complaint of an advocate Vivekanand Gupta.
Gupta, who is also Mumbai BJP secretary, lodged a complaint that Darekar and other office-bearers have misused their positions in the bank since 1998 and caused a loss of Rs 123 crore to the financial institution.
The investigation was taken over by the Economic Offence Wing (EOW) of the Mumbai Police, which specialised in probing embezzlement cases.
Darekar was earlier a member of Maharashtra Navnirman Sena (MNS). However, he joined BJP after losing the 2014 Maharashtra Assembly polls.
Gupta claimed he had lodged the first written complaint with the police in January and then in August last year, following which an inquiry was initiated in the matter.
The FIR was registered as the inquiry suggested that there was prima facie a criminal case, police said.
Meanwhile, Darekar said the case was the outcome of "political conspiracy" against him with an eye on the bank elections to be held on May 9.
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