The submarine Soryu was in the process of surfacing about 27 nautical miles (50 kilometers) south of Cape Ashizuri on Japan's southwestern island of Shikoku when it collided with the commercial ship, the Maritime Self-Defense Force said in a statement.
There was slight damage to the submarine's mast but it was able to continue sailing on its own, it said.
The navy did not identify the commercial ship, but NHK public television said it was the Hong Kong-registered bulk carrier Ocean Artemis. It was transporting 90,000 tons of iron to Okayama in western Japan after leaving the Chinese port of Qingdao last Friday with 21 Chinese crewmembers, it said.
Defense Minister Nobuo Kishi told reporters that the collision was “extremely regrettable.”
He said the submarine temporarily lost communication signals due to the damage to its antenna mast.
The commercial ship left the scene but later told Japanese coast guard officials that it sustained no damage and its crew did not even feel the impact, Kishi said.
He said the cause of the accident wasn't known and an investigation is underway.