The wreckage was found on the northern island of Hokkaido, where the LR-2 reconnaissance craft disappeared from radar Monday near Hakodate airport.
It had been flying there to pick up a hospital patient at the request of Hokkaido's governor.
Troops and emergency crews earlier Tuesday found debris spread widely over the mountainous area, with television footage showing trees levelled.
Parts shown included a damaged frame with a red circle resembling the Japanese national flag and used as a symbol of the nation's Self-Defence Force.
The propeller aircraft was scheduled to take the patient from Hakodate to Sapporo, Hokkaido's capital city, for special medical treatment.
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