The US military told Japanese authorities that their CH- 53 transport helicopter "landed" before the fire erupted in the early evening just outside a training ground on the island, said Itsunori Onodera.
National broadcaster NHK showed dramatic footage of firefighters battling orange flames after dark and plumes of black smoke billowing into the sky.
"When the US Marine Corp CH-53 helicopter landed, a fire started. We have received information that all crew members were safe," Onodera told reporters.
"Accidents by the US Marine Corps are continuing. We want to communicate to the US side that we demand safe operations," Onodera said.
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According to eyewitnesses cited by NHK, the accident occurred shortly after 5:30 pm (local time).
Officials from the US Marines based in Okinawa could not immediately comment.
In December, five crew members aboard a US Marine MV-22 Osprey were injured after what the Pentagon described as a "mishap" resulting in the plane landing in shallow water off Okinawa.
The deployment of Ospreys in Japan has prompted protests by Okinawa residents after a series of accidents in other countries involving the hybrid aircraft.
In August, US Marines were forced to mount a major search and rescue mission after an MV-22 Osprey crashed of the east coast of Australia.
They rescued 23 out of the 26 personnel and eventually called off the hunt for the three remaining crew.