Two Chinese coastguard ships entered Japanese waters on Saturday and sailed for more than one hour near Okinoshima Island and Tsushima Island off the southwestern main island of Kyushu.
The Japanese Coast Guard said this is the first confirmed entry by Chinese government vessels into the area.
The Japan Coast Guard asked the ships to leave the territorial waters, though it did not clarify whether it considered their presence an intrusion.
According to the coastguard, it was notified by the Defence Ministry that one Chinese coastguard ship entered territorial waters near the southern tip of Tsushima Island around 11.50 a.m. The ship left the waters around 12.20 p.m. after the coastguard called on the ship to leave by radio.
Tsushima Island is located about half way between the southern tip of the Korean Peninsula and the northwest coast of Kyushu, Japan's westernmost main island.
Under the U.N. Convention on the Law of the Sea, vessels of every country have the right to sail through territorial seas as long as they do not harm the safety of the countries concerned.
But the coastguard confirmed this ship and another Chinese vessel entered waters some 19 km north of Okinoshima Island around 3.50 p.m. The two exited the waters soon after 5 p.m., the coastguard said, Japan Times reported.
Tensions have been high over the Senkaku islands in the East China Sea, which China calls Diaoyu islands and the incidents of face-off between Chinese and Japanese ships are quite often. Diaoyu Islands in the East China Sea are a group of uninhabited islets controlled by Tokyo but claimed by Beijing.