The salary will be deducted over six months.
The strike, for salary hike as per the recommendations of the seventh pay commission, lasted four days.
"Following the high court's order which declared the strike as illegal, an action has been initiated and the legal section has issued a circular in accordance with the law to deduct 36 days' salary of the staff who resorted to agitation and put the corporation and lakhs of passengers in trouble," a senior MSRTC official told PTI.
They employees will be paid for only 24 days (while they work for 30/31 days) over the next six months.
The action was being taken as per the industrial dispute laws, and the high court's order declaring the strike as illegal mandates the MSRTC to take the action, the official said.
The Bombay high court, in response to a petition, had asked the employees to end their stir immediately.