The Maritime Self-Defense Force lost contact with the SH60J patrol chopper carrying four crew around 10:50 pm Saturday, said the official, with the navy handling the search-and-rescue mission.
Rescuers found one of the four men and the helicopter's flight recorder shortly after it went missing in northern waters off Aomori Prefecture, the official told AFP.
"There will be an investigation on what happened," he said.
"One of them has been rescued and the flight data recorder has been recovered. Analysis will be done on that," he told AFP.
The rescued man was uninjured and the helicopter issued a distress signal immediately after it lost contact, according to national broadcaster NHK.
Japan's military and coastguard are using a total of seven vessels and 10 aircraft to look for the missing men, the navy official said.
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