None of the 161 passengers and six crew members were injured and no damage to the plane was reported after the incident late Saturday, Jiji Press and Kyodo News agency said.
Japan’s transport ministry however considered it a serious incident that could have caused a disaster, and sent investigators to the scene, local media said.
Neither the airline nor aviation authorities could be reached for comment.
The pilot was able to put the brakes on manually, but the plane overran for about 66 meters (216 feet) and only stopped after entering a grassy area at Shonai Airport, northern Japan.