A police helicopter located the crashed copter on a snowy mountainside in Nagano prefecture in central Japan, public broadcaster NHK and other media reported.
"We've heard that three people were found in a cardio-respiratory arrest, but six others have not yet been found," an official with the Fire and Disaster Management Agency said.
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Officials in Japan normally do not confirm deaths until medical authorities have examined the bodies.
The nine people on board were rescue workers and local government officials who took off for a mountain rescue drill, local reports said.
The official said local police and officials are searching for the six others.
Aerial footage from NHK showed the badly damaged helicopter on the wintry mountainside.
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