One crew member who had been recovered from the waters was later pronounced dead, while rescuers searched for seven others who are still missing.
The two SH-60K choppers from the Maritime Self-Defense Force were carrying four crew each and lost contact late Saturday near Torishima island about 600 kilometres south of Tokyo.
The cause of the crash was not immediately known, but officials believe the two helicopters "highly likely" collided with each other before crashing into the water, Mr Kihara said.
He added his ministry will suspend training flights for all SH-60s for now.
Rescuers have recovered a flight data recorder, a blade from each helicopter, and fragments believed to be from both choppers in the same area, signs that the two SH-60Ks were flying close to each other.
Officials will analyse the flight data to try to determine what led to the crash.
Search and rescue efforts for the missing crew were expanded on Sunday, with the MSDF and Air Self-Defense Force together deploying 12 warships and seven aircraft.
Japan Coast Guard patrol boats and aircraft also joined the operation.
Mr Kihara said that the two helicopters were on night-time anti-submarine training in the waters. One lost contact at 10:38pm and sent an automatic emergency signal a minute later.
They lost contact about 270 kilometres east of Torishima island.
Only one distress call was heard — another sign the two helicopters were near the same place, because their signals use the same frequency and could not be differentiated, Mr Kihara said.
Defence officials said Saturday's training only involved the Japanese navy and was not part of a multinational exercise. They said no foreign aircraft or warships were spotted in the area.