A spokesman for Japan's Self-Defense Force (SDF) confirmed the late Saturday incident and said that one person was rescued but later confirmed dead.
Defence Minister Minoru Kihara said rescuers "spotted what are believed to be part of the aircraft in the sea, and we believe that the two helicopters crashed."
"At this point the cause is unknown, but firstly we do our best to save lives," Kihara told reporters, NDTV reported.
He said the helicopters were "doing drills to counter submarines at night".
Hours later, Kihara told reporters that the crew member who was rescued "was confirmed dead," according to the spokesman.
He also said the ministry retrieved flight recorders and was "analysing (the cause of the incident) including possibility of a collision between the two."
The helicopters appear to have crashed during night-time training off the Izu Islands in the Pacific Ocean, broadcaster NHK reported.
MP/PR