The Taipei Times said up to 100 Taiwanese fishing boats, escorted by 10 Coast Guard ships, were on a protest voyage to the Tiaoyutai Islands, which are called Senkaku in Japan and Diaoyu in China.
Organizers of the flotilla said the journey was aimed at asserting local fishermen's rights to operate in what they called their "traditional fishing grounds."
Japan's Kyodo News reported the Taiwanese vessels entered Japan's territorial waters Tuesday morning off Uotsuri Island, one of the Japanese-controlled Senkaku Islands, the first such intrusion by Taiwanese ships since Japan nationalized the islands on Sept. 11. Japan and Taiwan do not have diplomatic ties.
China's official Xinhua news agency said the Taiwanese boats were expected to return to port in Taiwan on Wednesday.
Xinhua said while sailing to the islands, the Taiwanese boats evaded Japanese vessels that attempted to stop them with water cannon.
Prior to leaving Taiwan, Coast Guard Administration Minister Wang Jinn-wang told lawmakers that if Japanese ships tried to spray water on their boats, "we will spray water back at them," the Taipei Times reported.
Wang also was quoted as saying his agency would not partner with China in protecting its fishing rights and that it would abide by the precepts of "no provocation, no conflict and no evasion," the report said.
The Taipei Times reported a member of the main opposition party had said it would not be in Taiwan's interests to assert its claim when China was already doing all it can to strengthen its sovereignty over the islands.
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