The suspension was ordered this evening by the minister who is currently in New Delhi on an official trip.
The issue of RFID cards was raised during the recently held assembly session.
"There are certain irregularities in RFID card allocations that were brought to my notice due to which the suspension is ordered.
"There are other issues too but I might not discuss them at this juncture," Palyekar told PTI today.
He has also ordered the department to hold back the payment of the agency which was awarded contract to supply RFID cards to the fishermen, who are usually employed on the trawlers.
The minister on the floor of the House had assured to conduct an inquiry into delay and irregularities in providing the RFID cards to the fishermen.
Opposition MLAs including NCP's Churchill Alemao and Congress' Francis Silveira had raised the issue during the assembly session.