Several Japanese Coast Guard ships fired water cannon and shouted warnings at a boat carrying Taiwanese activists who were attempting to land on islands disputed by Taiwan, Japan and China, a spokesman said.
Through loud speakers, the Japanese Coast guard urged the activists and four Taiwanese Coast Guard vessels accompanying them, to retreat from waters around the islands, which are known as the Senkakus in Japan, and Diaoyu in China.
The deterrent worked and the Taiwanese ships left the area, the Japanese Coast Guard said.
According to state news agencies in Taiwan and China, the confrontation occurred about 28 nautical miles from the islands in the East China Sea.
Several activists were aboard the main protest boat, Chinese news agency Xinhua said, adding that it was the third time since June 2008 that the ship had been involved in a confrontation with the Japanese Coast Guard.
Once on the islands, the activists planned conduct ceremonies relating to Matsu, the "Goddess of the Sea" on the islands, according to the Li Yiqiang, secretary general of World Association for Protecting the Diaoyutais.
The activists included Hsieh Mang-lin, chairman of the Chinese Association for Protecting the Diaoyutais. He told Taiwan's Central News Agency (CNA) that they planned to erect a statue of Matsu on the island to help protect Taiwanese fisherman operating in the area.
According to CNA, the Taiwanese fleet set out at 1.45 a.m. local time Thursday from Shenao in New Taipei and planned to return home the same afternoon.
Disagreement over who owns the islands strained relations between Japan and China during the latter half of 2012, and the dispute shows no signs of waning.
Protests flared across China in September, soon after Japan announced it had bought the islands from private Japanese owners. The deal was struck in part to prevent the islands being bought by Tokyo governor Shintaro Ishihara who had called for donations for a public fund to buy them.
China was outraged, as were protesters who marched through several Chinese cities calling for boycotts of Japanese products and urging the government to give the islands back.
In December, the dispute escalated when Japan scrambled fighter jets after a Chinese plane was seen overhead. A number of Chinese ships have also entered contested waters despite warnings from the Japanese Coast Guard.
China says its ownership dates back hundreds of years. However, Japan claims that China ceded sovereignty of the islands in 1895 when it lost the Sino-Japanese war. Japan then sold the islands in 1932. During the WWII, the U.S. administered the islands but returned them to Japan in 1972 as part of its withdrawal from Okinawa.