Japan Wednesday filed a formal protest with Beijing over the incident in the islands which are claimed by both countries. China calls the islands Diaoyu Islands, and maintains it has "indisputable sovereignty" over them.
Japanese Vice Foreign Minister Kenichiro Sasae filed the protest after summoning Chinese Ambassador Cheng Yonghua to the Foreign Ministry, said a Kyodo News report carried by the Japan Times. Officials quoted Sasae as saying the brief intrusion was "extremely serious" and "unacceptable."
The Japanese Coast Guard said Chinese fisheries vessels entered Japanese waters off the islet of Kuba in the East China Sea early Wednesday.
The incident comes days after the Japanese government revealed plans to nationalize the uninhabited islands by purchasing parts of them from their Japanese owner, the report said.
Japanese foreign ministry officials said Sasae told the Chinese ambassador it was regrettable the ships had entered Japanese waters although Japan had protested a similar incident in March.
The Yomiuri Shimbun quoted Sasae as telling the Chinese envoy: "We can't regard (the incident) as innocent passage allowed under international laws, and our country won't tolerate it. We strongly protest and strongly demand measures to prevent a recurrence."
Separately, Japanese Chief Cabinet Secretary Osamu Fujimura repeated his country's position that "the Senkaku Islands, historically and based on international law, are an integral part of Japanese territory," Kyodo reported. The islands are officially part of the city of Ishigaki in Okinawa Prefecture.
China's official Xinhua News Agency reported the ships were patrolling the waters near the islands as traditional Chinese fishing grounds.
The incident comes as foreign ministers of Japan and China met in Phnom Penh, Cambodia, on the sidelines of the Association of South-East Asian Nations (ASEAN) meeting that opened Thursday. The regional meeting itself it taking place at a time of growing concerns among some of its members over China's territorial claims including the South China Sea.
The China Daily, reporting Thursday on the Phnom Penh meeting between Chinese Foreign Minister Yang Jiechi and his Japanese counterpart Koichiro Gemba, said Beijing's "principled position" on the Diaoyu Islands was reaffirmed and quoted analysts as saying Tokyo was only seeking to divert attention from unpopular measures.
The report said Beijing stressed its "indisputable sovereignty" over the Diaoyu Islands must be respected by Japan. The report said the fishing vessels arrived in waters near the islands for the first time since Japanese Prime Minister Yoshihiko Noda announced a plan to "nationalize" them.
The reports, citing analysts, said Noda should engage in damage control to avoid further harming ties with China.
Earlier this week, a senior U.S. State Department official said the islands fall within the scope of the 1960 Japan-U.S. security treaty, which requires the United States to defend Japan in the event of armed attack, Kyodo reported.
The Yomiuri Shimbun reported the Japanese government wants to purchase Uotsurijima, Kita-kojima and Minami-kojima islands of the Senkaku Islands, currently owned by a civilian.