The Air Self-Defense Force's T-4 training aircraft crashed near a lake in central Japan's Aichi region immediately after taking off at its Komaki Air Base last week.
"The deaths of its two crew members were confirmed today," Hiroaki Uchikura, head of the ASDF, told a news conference.
"It is gut-wrenching that we lost these precious lives of our comrades," Uchikura said.
A search after the crash soon led to the discovery of what appeared to be remains but officials could not immediately identify them.
However, "a subsequent official analysis confirmed, much to our sorrow, that these belong to two soldiers on board that we had been looking for", Uchikura said.
He said he "takes the accident seriously" and "will do our best to identify the cause and improve aviation safety".
The T-4 seats two and is a "domestically produced, highly reliable and maintainable training aircraft... used for all basic flight courses", according to the defence ministry website.
Aerial footage of the lake soon after the crash broadcast by NHK showed an oil slick on its surface dotted with what appeared to be debris.
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