The islands, called Senkaku in Japan and Diaoyu in China, are controlled by Japan but claimed by China and Taiwan.
Tension in the region has been high since Japan’s purchase of the islands from their private Japanese owner.
Taiwanese vessels, including coastguard ships, have now left the area.
Meanwhile Japanese Vice-Foreign Minister Chikao Kawai, who is in Beijing for a two-day visit, is meeting Chinese counterpart Zhang Zhijun, amid a row that has seen anti-Japanese protests in several Chinese cities.
Chinese surveillance and fishing boats have also been sailing in and out of waters around the islands in recent days, following the Japanese government’s announcement that it had bought the islands.
The row over ownership of the islands has been rumbling for years and has flared sporadically.
A spokesman from Taiwan’s Coast Guard Administration said that 58 fishing vessels arrived in the disputed waters at around 05:00 a.m. local time after setting off from a northern Taiwanese port on Monday afternoon.
The fishing boats were accompanied by several Taiwanese coast guard vessels.
Japan’s coast guard said warnings were issued to the boats and television footage showed water being sprayed towards the Taiwanese ships.
The flotilla turned back towards Taiwan after being in the area for a few hours, reports said.
The move to sail to the disputed area, activists and fishermen said, was to protect fishing rights and access to traditional fishing grounds.
“Fishing rights are more important than sovereignty, but fishing rights also means sovereignty [in this case],” activist Chen Chunsheng, who is organizing the flotilla, told reporters on Monday.
”So for this day on which we negotiate fishing rights, we are willing to be the backing of the government.”
Both China and Taiwan say they have inherited historic sovereignty over the islands.
The Japanese government moved to buy the islands in response to a potentially much more provocative plan by right-wing Tokyo Governor Shintaro Ishihara to buy and develop them using public donations.
The row comes at a time when both China and Japan are facing political changes domestically, making it difficult for either side to be seen as backing down.
Japanese Prime Minister Yoshihiko Noda’s government – already hit by poor figures in opinion polls – is likely to face an election in coming months. China is due to hold a party congress in weeks that will see major changes in the top echelons of leadership.
Arriving in Beijing on Monday, Japan’s envoy Chikao Kawai stressed the importance of bilateral ties.
“Because of the current difficult situation, I plan to explain what Japan is now considering to Zhang Zhijun and listen to what China is considering, for the importance of the relationship between both countries,” he said.
Chinese Foreign Ministry spokesman Hong Lei said Beijing would set out its position: “China will urge Japan to correct their mistakes and make efforts in improving ties,” he said.
A ceremony to mark 40 years of ties with Japan – due on Thursday – has been put off.
Last week, several major Japanese companies briefly suspended operations in China after attacks on shops and car dealerships.
This led to fears over a larger impact on trade between China and Japan, which is worth about $345 billion.
Most Japanese companies have resumed their operations in China. But China’s customs officials are to step up inspection of Japanese air cargo arriving at Beijing airport, said a Kyodo news report citing unnamed Japanese businesses sources.
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