The Sri Lankan Navy in a statement said the arrests occurred during a special operation in the sea area north of Mannar.
On a two-day visit, the submarine was welcomed by the Sri Lanka Navy.
The Maritime Rescue Coordination Centre (MRCC), responsible for coordinating and facilitating maritime search and rescue operations in its designated region as well as neighbouring regions conducted the search operations, a Sri Lanka Navy statement said on Tuesday.
The fishermen were arrested on Monday evening in a joint operation by the Navy and the Sri Lanka Coast Guard off the coast of Karainagar in the northern Jaffna peninsula, the statement said.
President Wickremesinghe will attend the handover ceremony, the Sri Lankan Airforce spokesman Captain Dushan Wijesinghe said.