According to the Kyodo news agency, three members of the submarine crew are feared injured, while the private vessel was left unscathed.
The fishing boat was hit while the submarine was surfacing, the Japan Maritime Self-Defence Force confirmed.
In 2001, US submarine the USS Greeneville and Japanese fishing training vessel the Ehime Maru collided in a major incident that left nine Japanese citizens dead, including four high school students. A year after the collision, the US government signed an agreement to pay around $11.4 million in compensation.
