Six Chiese ships enter waters near disputed islands
China said the ships were carrying out "law enforcement" to demonstrate its jurisdiction over the islands, known as Diaoyu in China and Senkaku in Japan, BBC reported.
At least two of the vessels left after the Japanese coast guard issued a warning, Japanese officials say.
The move came after Japan sealed a deal to buy three of the islands from their private Japanese owner.
Japan controls the uninhabited but resource-rich East China Sea islands, which are also claimed by Taiwan.
The Japanese Coast Guard said the first two Chinese boats entered Japan's territorial waters at 06:18 local time (21:18 GMT Thursday), followed by another fleet of four other ships just after 07:00.
The first two ships then left the area. A third ship left later on Friday morning, one report said. No force was used, Japanese officials added.
Japanese Prime Minister Yoshihiko Noda has established a task force to address the issue. The government also summoned the Chinese ambassador, Cheng Yonghua, to lodge a protest.
"We understand that the dispatch of six ships is surely an unprecedented case, considering past incidents," Chief Cabinet Secretary Osamu Fujimura said.
He added that Japan asked China to "secure the safety" of its nationals after a report from its Shanghai consulate that a Japanese group was "assaulted by Chinese" at a restaurant.