The 10,833-tonne Cygnus Ace immediately reported the collision to the coast guard and said its radar was not able to locate the South Korean vessel, AFP writes.
The 4,255-tonne-Orchid Pia has not responded to radio signals from the coast guard, which has launched six patrol vessels and two planes to search the freighter.
The ship was laden with 5,051 tons of steel coils and was travelling from the port of Kashima in eastern Japan to South Korea, the coast guard said.
'It is possible that Orchid Pia sunk,' a coast guard official said. 'We found an empty raft in the area waters, but so far we are continuing the search for the missing individuals,' he said.
Cygnus Ace suffered some damage but is able to navigate, the coast guard said. There are no reports of sailors missing from the ship.