Japan has lodged a protest with the Chinese ambassador in Tokyo, after a Chinese ship sailed close to contested islands in the East China Sea.
Japan administers the uninhabited Senkaku islands, which China also claims under the name Diaoyu islands.
Russian naval ships were also spotted in the area at the same time, Japanese local media said.
In 2012, relations between Japan and China deteriorated after Japan bought the islands from a private owner.
The islands are important because they are close to key shipping lanes, offer rich fishing grounds and lie near potential oil and gas reserves.
Reacting to the incident, Japan’s Chief Cabinet Secretary Yoshihide Suga expressed “serious concern” at a news conference, saying it would escalate tensions.
Prime Minister Shinzo Abe has told his government to work closely with the US and other countries to deal with this, Mr Suga said.