's navy tracked a submarine that intruded into its waters for nearly two hours and then lost track of it without identifying its nationality, a military official said.
The Naval vessel Atago spotted the submarine in Japanese waters at 6.56am (0756 AEST) but the craft did not raise a national flag or surface, breaching international laws, a defence ministry spokesman said.
Atago, an Aegis-equipped warship, chased the submarine off the coast of Kochi prefecture in western Japan, facing the Pacific Ocean, until about 8.40am (0940 AEST) , he said.
Using sonar, Atago confirmed that the submarine does not belong to the Japanese navy nor its ally the US Navy, he said.
It was the first time in four years that a foreign submarine had intruded into Japanese waters, according to the official.
In November 2004, a Chinese nuclear-powered submarine entered Japanese waters. apologised less than a week later.