The helicopter, a CH-53, came down in the Okinawa region near the village of Takamura Takae on Wednesday morning, local media reported.
Images taken from the scene showed the aircraft engulfed in a fireball with thick black smoke pouring into the sky.
It is not yet known if anyone was hurt in the crash.
It came hours after the US sent six military aircraft including two supersonic bombers to the Korean peninsula in a show of force.
The bombers from Guam staged a simulated air-to-ground missile firing drill with two South Korean F-15K fighters over the East Sea.
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Japan also sent two military aircraft as tensions mount the North could trigger World War 3.
This story is being updated.