TOKYO — The Japanese Coast Guard used water cannons on Tuesday to disperse fishing boats from Taiwan in waters claimed by Japan in the East China Sea, widening a territorial dispute that has already pitted Japan against China and threatened vital trade relations in the region.

Japan’s top government spokesman, Osamu Fujimura, said Tokyo had lodged a protest with Taiwan’s government over the fishing boats’ intrusion into waters around a chain of small, rocky islands controlled by Japan, but also claimed by China and Taiwan. Japanese ships have also confronted fishing boats from mainland China in the area in recent days.

The islands, called the Senkaku Islands in Japan and the Diaoyu Islands in China, are uninhabited, but the waters around them are coveted fishing grounds and may have large gas reserves. The status of the islands touches on historical grievances in East Asia dating from World War II and before.

Taiwan’s government generally maintains friendly relations with Japan, and has not been very vocal about its claim to the islands. Even so, activists in Taiwan have raised their voices about the issue as mainland Chinese activists have done.