The Chinese Foreign Ministry said the flotilla, in two fleets, entered the disputed waters to conduct maritime surveillance near the islands known as Senkaku Islands in Japan and the Diaoyu Islands in China.
"The patrol missions demonstrate our government's jurisdiction over the Diaoyu Islands and affiliated islands, and safeguard our country's maritime rights," the ministry added.
The Japanese coastguard ordered the Chinese deployed ships to leave the waters, where huge maritime gas and oil fields exist, but only three complied.
"We lodged a strong protest and also we made a strong case that the Chinese side should leave from the territorial waters around the Senkaku islands," Japanese Foreign Minister Koichiro Gemba told a media conference in Sydney, Australia, after talks with Australia's foreign and defense ministers.
"I'd like to underscore that we should never let the situation escalate and we have strong hopes for the Chinese to respond in an appropriate and calm manner," added Gemba, who said he would return to Tokyo a day earlier than planned.
No force had been used to expel the remaining vessels, a coastguard official said.
The action adds to recent tensions over the group of islands and comes after China submitted charts showing the base points and baselines to the United Nations on Thursday in support of its claim to ownership of the islands and surrounding waters.
Publishing the charts "demonstrates China's sovereignty over the islets…in accordance with its law on territorial seas and adjacent zones," reported the Chinese Xinhua news agency.
"China has now fulfilled all the obligations as stipulated in the United Nations Conventions on the Law of the Sea and has completed the whole legal process…," Xinhua added.
The news agency quoted a senior Chinese military official as urging the army to be "prepared for any possible military combat." The report made no mention of the territorial dispute with Japan.
"Efforts should be made to ensure that the military is capable of resolutely performing its duty to safeguard the country's national sovereignty, security and territorial integrity whenever it is needed by the Party and the people," Xu Caihou, vice chairman of China's powerful Central Military Comission said.
Earlier this week, the Japanese government bought three of the five disputed islands for two billion yen (19.8 million euros, $25.7 million), in what it says was a move to prevent the islands being acquired by city of Tokyo and its nationalist Governor Shintaro Ishihara.
The government decided to purchase the islands after Ishihara floated a plan to buy and build facilities on the islands.
The purchase angered Chinese authorities and sparked anti-Japanese protests in several cities. Dozens of people protested outside the Japanese ambassador's residence in Beijing on Thursday.
The group of islands were at the center of a dispute between Beijing and Tokyo in 2010 after Japanese authorities arrested a Chinese trawler captain whose boat collided with Japanese coastguard vessels near the area.
jlw/tj (dpa, AP, AFP)