A total of six passengers were on board the helicopter heading to a hospital in Fukuoka city from Tsushima Island in the Nagasaki region on Sunday afternoon.
A few hours after losing communication, the six passengers were found by a patrol ship along with the helicopter.
The other three people, found holding on to the helicopter, were conscious, it added.
The national Maritime Safety Committee will carry out investigations, he added.
According to the Asahi Shimbun daily, a helicopter operated by the same company crashed into farmland in the Fukuoka region, killing two people on board, in July last year.
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