Japan's coastguard on Sunday arrested the captain of a Chinese fishing boat that allegedly intruded into Japanese territorial waters, a report said.

The 47-year-old captain was arrested on charges of violating fishing laws in Japan's exclusive economic zone, Jiji Press said, citing the coastguard.

The coastguard's regional headquarters in the city of Nagasaki said its patrol ship spotted two Chinese fishing boats in waters close to the Goto Islands, off Japan's southwestern coast, the report said.

After the two vessels rejected its order to stop for on-board inspections, the patrol ship chased one of the two for nearly four-and-a-half-hours.

Japan-China relations plunged to their lowest level in years in September 2010 when a Chinese trawler rammed two Japanese coastguard patrol boats near disputed islands in the East China Sea, called Senkaku in Japan and Diaoyu in China.

The coastguard arrested the Chinese boat's captain and held him for 14 days.

China reacted with fury, issuing protests, scrapping meetings and cultural events in a diplomatic offensive that continued after Japan freed the captain while nationalist sentiment sparked street protests in both countries.

Earlier this year the two countries agreed to improve ties following the incident.

But in September Japan's new Foreign Minister Koichiro Gemba voiced concern over China's growing naval power and its activities near the disputed islands.

The territorial row intensified in August after Japan protested to Beijing over the entry of Chinese fishery patrol boats into waters near the islands.

The string of five small islands lies between Japan's far-southern Okinawa island and Taiwan in an area believed to hold seabed oil deposits.

Controlled by Tokyo, but also long claimed by Beijing and Taipei, the uninhabited islands have often sparked regional tensions.