The helicopter 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.
The incident, which occurred shortly after US military drills over the Korean peninsula, led to speculation that North Korea could have shot down the helicopter.
Pyongyang has previously vowed to fire at any US aircraft flying near its territory.
Police headed to the crash site, which lies southwest of the Korean peninsula, at around 6pm local time (10am GMT).
It it thought the vehicle was a CH-53E Super Stallion, a large transporter helicopter that is the heaviest in the US fleet.
Around 54,000 US military personnel are based in Japan at facilities including an Okinawa base.
Police said seven people had been on board the helicopter but none had been injured.
The US confirmed the helicopter was based at the US Marines’ Futenma airstrip.
It reportedly burst into flames after crash-landing.
It came hours after the US sent six military aircraft including two supersonic bombers to Korea 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.
Japan also sent two military aircraft as tensions mount the North could trigger World War 3.
Last month, Kim Jong-un’s tyrannical regime threatened to blast American planes out of the sky after accusing Donald Trump of declaring war with his Twitter threats.
Foreign Minister Ri Yong-ho said: “The whole world should clearly remember it was the US who first declared war on our country.
“Since the United States declared war on our country, we will have every right to make countermeasures, including the right to shoot down United States strategic bombers even when they are not inside the airspace border of our country.”
Mr Trump has suggested in recent days that military action could be the only way to solve the North Korea crisis.
Japanese military admitted today a US Navy aircraft carrier, the Ronald Reagan, was conducting drills with one of its own in waters around Okinawa.
The exercise with the Reagan strike group, which began on Saturday, involves vessels sailing from the Bashi Channel, which separates the Philippines and Taiwan, to seas around Japan’s southwest island nearer to North Korea.
One Japanese destroyer, the Shimkaze, is accompanying the 100,000-tonne Reagan, which is based in Japan, and its escort ships.