The statement comes after protests spread to dozens of Chinese cities.
China sent the boats to the islands, called Diaoyu in China and Senkaku in Japan, after Tokyo sealed a deal to buy three of the islands.
US defence secretary Leon Panetta, who is in Tokyo for talks, has called for restraint on both sides.
"A misjudgement on one side or the other could result in violence, and could result in conflict," said Mr Panetta, who is also due to travel to Beijing this week.
Leon Panetta arrived in Japan for a short, but timely, visit. The mounting tension between his hosts and China is expected to dominate his meetings with the foreign and defence ministers.
Panetta will travel next to China, where he may be the last high-ranking US official to visit before the country's once-a-decade leadership change.
Ultimately, who is right on the territorial dispute? As far as the Obama administration is concerned, it's not about who owns the islands - it's about avoiding a costly action/reaction scenario that could lead to conflict between the two countries.
As US Secretary of State Hillary Clinton said on her recent trip to the region, and Mr Panetta has reiterated, the US doesn't want to get involved in other nations' territorial disputes. However, while the relationship between the world's second and third largest economies, China and Japan respectively, tends to be somewhat strained - genuine unrest would be an international problem.
China, meanwhile, is maintaining its sovereignty over the uninhabited but resource-rich islands in the East China Sea which are controlled by Japan and also claimed by Taiwan.
The China Marine Surveillance (CMS) - which sent the boats on Friday - will continue with the ''law enforcement activities'' around the disputed islands, Chinese state media reported.
''These law enforcement and patrol activities demonstrated China's jurisdiction over the Diaoyu Island and its affiliated islets, achieved the goal of demonstrating China's sovereignty claim and ensured the country's maritime interests," Xiao Huiwu, deputy chief of the headquarters of CMS told Xinhua news agency.
Anti-Japanese protests swept across China over the weekend, with thousands of protesters targeting Japanese-made cars and burning Japanese flags.
On Sunday, hundreds of Chinese protesters faced off against riot police at the Japanese embassy in Beijing.
Japanese Prime Minister Yoshihiko Noda has urged Beijing to take steps to protect Japanese nationals, adding that the authorities in both countries should "remain calm".
The tension between the two countries has also hit trade relations and sparked off fears of wider economic implications.
Japanese electronic giant Panasonic is suspending operations at its factory in Qingdao until Tuesday after the plant was damaged by protesters on Saturday, Japanese media reported.
Mr Panetta is expected to address the conflict with both nations during his visits, which are part of an Asian tour that will also include New Zealand.
Washington did not take a position with regard to the territorial disputes in Asia but would appeal for restraint on both sides, he said.
The islands have long been a point of contention, but the most recent row in the past week heightened tension and led to fears of potential naval conflict.
Analysts see Japan's decision to buy the islands as damage limitation in response to a much more provocative plan by the nationalistic governor of Tokyo, who wanted to purchase and develop them.
In Japan, the government seems unlikely to back down with an election looming.
There is talk in the Japanese press that some on both sides could be willing to risk a limited naval clash in defence of the conflicting claims, correspondents say.
Further complicating matters, Japan's newly appointed ambassador to China, 60-year-old Shinichi Nishimiya, died on Sunday, the foreign ministry said.
The envoy - who had been due to take up his post in October - collapsed several days earlier near his Tokyo home and was taken to hospital.
The foreign ministry has not publicly commented on what caused his death.
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