Workers have also been asked to co-operate in moving oil stocks, an official said.
SLPA is planning to covert the tank farm to a common user facility.
Lanka Marine Services (LMS), a unit of JKH, was ordered by court to hand over a land containing a tank farm to Sri Lanka Ports Authority (SLPA), following a ruling in which the group was faulted over the privatization of the bunkering unit.
LMS also has to pay compensation - to be determined by the Commissioner of Labour - workers whose services are terminated.
The company has to deposit compensation in a bank.
Earlier reports had indicated that LMS workers would be absorbed by the Jaye container terminal of the SLPA.
The order had said any oil remaining in the tanks after September 12 would remain with Sri Lanka Ports Authority, lawyers said.