'No force'
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.
"Our patrol vessels are currently telling them to leave our country's territorial waters," the coast guard said in a statement.
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.