Dozens of Taiwanese fishing boats entered waters near the Diaoyu Islands in the East China Sea yesterday before leaving at about noon after Taiwanese coastguard vessels exchanged water cannon blasts with the Japanese coastguard.
"We have made contact with the Taiwanese authorities, and told them that they cannot enter our territorial waters," Japan's chief cabinet secretary, Osamu Fujimura, said. "This is something that needs to be solved in the context of good bilateral ties between Japan and Taiwan."
The two parties have no official diplomatic relations, with Japan having established diplomatic ties with Beijing 40 years ago this week.
The altercation, which was shown on Japan's NHK public television network, occurred after about eight Taiwanese patrol ships escorted dozens of fishing boats near Diaoyu Island, the largest of the disputed islands, called Uotsuri Island in Japan.
Beijing and Taipei both argue they have inherited China's historic sovereignty over the islands, which Japan calls the Senkakus.
The footage showed Japanese vessels racing up alongside a Taiwanese fishing boat and spraying it with water, while Taiwanese coastguard ships sprayed water back at them.
At the weekend, before the fishing boats set sail, Chen Chun-sheng, the head of the Suao Fishermen's Association in Taiwan, said: "Tiaoyutai [the Diaoyu Islands] has been our traditional fishing ground for centuries.
"We pledge to use our lives to protect it or we'd disgrace our ancestors."