“The F-16 jet crashed some 470 nautical miles north-east of Nemuro,” a spokesman at the Japan Coast Guard said.
“The pilot ejected and is now waiting for rescue at sea.”
The crash happened around 11:30am (local time), and coast guard ships and plane are now heading to the accident site.
The city of Nemuro is 1,000 kilometres north of Tokyo.
The US military was not immediately available for comment.