Three crew members from the Maritime Self-Defense Force submarine Soryu suffered minor injuries, and pictures from the Japanese Coast Guard showed it sustained damage to its fairwater planes, the winglike structures on its conning tower.
The accident occurred off the main island of Shikoku in southern Japan.
The Soryu, commissioned in 2009, is the first in its class of Japanese diesel electric-powered submarines. It displaces about 3,000 tons and has a crew of around 65.
The Defense Ministry said communications equipment on the sub was also damaged, although it was still able to operate.
“Soryu scraped the hull of the vessel as it was surfacing. It is extremely regrettable the MSDF submarine has collided with a commercial ship,” Defense Minister Nobuo Kishi said.
The commercial vessel — the Hong Kong-registered bulk carrier Ocean Artemis — reported no damage, Coast Guard officials added.
Bradley Martin, a RAND Corp analyst and former US Navy captain who analyzed images of the damage, said the impact would have restricted the submarine’s capabilities.
“I wouldn’t call the damage ‘minor.’ The submarine can’t dive and can’t communicate,” Martin said in an email to CNN.
The USS Greeneville was conducting an emergency surfacing demonstration for civilian guests aboard when it came up under the Japanese ship, the Ehime Maru, on February 9, 2001. The fisheries training vessel, carrying students and teachers from a fisheries high school in Uwajima, Japan, sank within minutes.
Rescuers saved 26 people.
The US Navy paid a total of $16.5 million in compensation to victims and families of those killed. The sub’s commander, Scott Waddle, was found guilty of dereliction of duty and negligent hazarding of a vessel by a military court of inquiry and forced to retire.