Six bodies were found in the morning inside the wreckage in the central prefecture of Nagano, a Nagano police spokesman told AFP.
Three others, including the pilot, were confirmed dead on Sunday after a police helicopter located the crash site on a snowy mountainside.
Bad weather halted rescue operations until Monday.
The government will send investigators to the area where the helicopter went down on Sunday, public broadcaster NHK reported.
The nine people on board the aircraft were rescuers and local government officials involved in a mountain rescue exercise, according to NHK and other media.
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