Besides former deputy chief minister Pawar, those accused in the case include NCP leader Jayant Patil and several senior cooperative bank officials from 34 districts in the state.
The accused allegedly were complicit in causing losses worth Rs 1,000 crore to MSCB between 2007 and 2011.
A subsequent inspection conducted by the National Bank for Agriculture and Rural Development (NABARD), and a charge sheet filed by a quasi-judicial inquiry commission under the Maharashtra Cooperative Societies (MCS) Act blamed Pawar and other accused, including several directors of the bank.
It said their decisions, actions and inactions caused such losses to the bank.
NABARD's audit report revealed breach of several banking laws and RBI guidelines by the accused in distribution of loans to sugar factories and spinning mills, and the subsequent default on repayment and recovery of such loans.
At that time, Pawar was the director of the bank.
However,despite the inspection reports, no FIR was filed in the case.
Local activist Surinder Arora filed a complaint with the EOW in the case in 2015 and approached the high court, seeking that an FIR be registered.
On Thursday, the high court held that prima facie, the NABARD's inspection report, the complaint, and the charge sheet under the MCS Act showed there existed "credible evidence" against the accused in the case.