According to the coast guard date, the incident took place at about 3:30 a.m. local time on Sunday (18:30 GMT on Saturday), NHK said, adding that the small ship overturned as a result of the collision.
Rescuers who arrived at the scene found the body of a man, whose death was confirmed by medical staff. Apart from him, there were supposedly two other people aboard, including a 12-year-old boy, who was rescued by a passing ship. The third person is still missing.
The cause of the collision is yet to be established.