The incident occurred at Paipra in Muvattupuzha Saturday night.
Of the total nine organisations of bank employees, three are taking part in the general strike.
The directive was issued considering the possibility of banks remaining closed for four days, Minister for Cooperation and Registration V N Vasavan said.
A high-level committee that probed the irregularities, however, reported that the bank has only Rs 7 lakh in its kitty.
The Rs 22,842 crore loan fraud of ABG Shipyard was unearthed by the CBI recently.
The RBI has allowed banks to increase the fee for ATM transactions beyond the free monthly permissible limit in order to offset higher interchange fee.
Shutters of branches across many parts of the country on Friday were down following the strike call given by the United Forum of Bank Union (UFBU), an umbrella body of nine bank unions.
As a result, services such as deposits and withdrawal at branches, cheque clearance and loan approvals might be affected due to the strike. But ATMs are expected to function as usual.
The FM said there was an urgent need to scale up banking to meet the growing industry needs and ensure that all economic centres are covered with at least one physical or digital banking presence.
The suspension order issued by bank president T A Niwas stated that the action was taken on the basis of the findings of the inquiry report prepared as per the Kerala Cooperative Societies Act