The boat, the Zheling Yuyun 622, fled after ignoring an order by a Japanese patrol ship to land off one of the Ogasawara islands, some 1,000 kilometres south of Tokyo, according to Japan's coastguard.
After a 12-kilometre, 85-minute "zigzag" chase, Japanese coastguard officials boarded the fishing boat and arrested its 31-year-old captain Zeng Yong, a coastguard statement said.
The ship's dozen-member crew was suspected of poaching corals, after about 100 Chinese boats were seen the area yesterday, it added.
Japanese media reports said there has been a swell in the number of Chinese fishing boats suspected of hunting red corals -- highly prized in China as jewelry -- since last month in waters off the Ogasawaras, also known as the Bonin islands.
Zeng was the fourth Chinese fishing boat captain arrested near the islands this month, a Yokohama Coast Guard official said.
The Japanese coastguard tends to chase off Chinese crews hunting corals in the area and the incidents rarely cause major friction between Tokyo and Beijing, although the countries are at loggerheads over an island chain in the East China Sea.
Earlier this month, the South Korean coastguard shot and killed the Chinese skipper of a fishing boat in a confrontation in the Yellow Sea, triggering an angry protest from Beijing.
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