TOKYO—A U.S. Marine Corps helicopter went up in flames after an emergency landing Wednesday on the southern Japanese island of Okinawa, the latest accident to raise concerns about the U.S. military presence there.

A U.S. military statement said no one was injured in the crash, which happened in the northern part of Okinawa outside of a U.S. training area. Footage from the scene aired on Japanese public broadcaster NHK showed smoke and flames billowing from the CH-53E helicopter on the ground while firefighters poured water...