Japan's coastguard confirmed that it was rushing to the crash site but did not supply further details. Broadcaster NTV said two crew were missing.
"We received a report that the aircraft fell in waters east of Okinawa's main island," a coastguard official said. "We have dispatched patrol boats and planes to the site at the request of the US military."
Okinawa is home to more than half of the 47,000 US service personnel stationed in Japan as part of a defence alliance.
Japan said last week it would temporarily halt work on a controversial new US military base in southern Okinawa as talks continue with local officials opposed to the project.