A Japanese cargo ship collided with a foreign-registered vessel in the Seto Inland Sea off the island of Shikoku in western Japan late on Thursday, national broadcaster NHK reported on Friday.
The Japanese ship capsized and sank about 2 hours and 40 minutes after the crash, the broadcaster said.
Nine of the 12 crew members onboard the Japanese freighter, the Byakko, were rescued but three were missing, NHK quoted the local coast guard as saying.
Coast guard rescue teams were searching for the missing, it said. The coast guard did not immediately respond to requests for comment.
The foreign ship, ULSAN PIONEER, had a total of 13 South Korean and Myanmar nationals on board, but the ship did not sink and no one was injured, NHK said.