The chopper was discovered ablaze on a bridge in the small village of Ueno, around 150 kilometres northwest of the capital Tokyo.
"Four people on board were found dead," a transport ministry official told AFP.
The AS332-L Super Puma helicopter was operated by the Toho Air Service, which confirmed that four male staff members were on board at the time of the accident.
An official with the local emergency services said the fire was extinguished at 3:21 pm , about an hour after officials spotted the accident.
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