The SH-60K helicopters, each crewed by four people, were conducting submarine location drills off the Izu Islands in the Pacific Ocean in April when they collided.
To date, only one body has been found while the other seven were declared dead in June by the Maritime Self-Defense Forces after a fruitless search operation.
A deep-sea probe by a national research institute that began this month led to the discovery of the two aircraft "on the seabed near the site of the crash", according to a navy statement released Monday.
"The seabed investigation is continuing, and we are assessing whether pulling up the bodies of the aircraft will be possible", it said.
While cognisant of the proximity to each other, the two helicopters "never attempted to avoid each other until the moment of the collision," suggesting lapses in standard lookout practices, a defence ministry report said earlier this month.
The report also concluded altitude control of the aircraft was "insufficient".
In April 2023, a Japanese army UH-60JA helicopter with 10 people on board crashed off Miyako island in southern Okinawa. There were no survivors.
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