The 4,300-tonne Mongolian-flagged ship carrying 16 North Korean crew sank in the international waters off the South's southern island of Geomun on Friday.
Two bodies were retrieved from the sea and returned to the North along with the three sailors across the border truce village of Panmunjom, Seoul's unification ministry spokeswoman told AFP.
Search operations involving the navy and coastal guard are still underway to find 11 missing fishermen.
Pyongyang yesterday asked for cooperation from "countries concerned" in rescuing survivors and helping them to return home.
The surviving crew reportedly told rescuers that the ship had suddenly listed sharply to one side.
South Korea has a protocol of sending back North Korean fishing boats straying across the maritime border or those rescued from sea accidents, unless they seek to defect.