Japan's coastguard said Tuesday it had arrested a Chinese boat captain in a possible fresh test for sometimes fraught maritime relations, just days after a South Korean officer was stabbed to death at sea.

A coastguard vessel pursued the fisherman's 130-tonne boat for over six hours after it was spotted lowering ropes into the water around four kilometres (2.5 miles) off islands in Nagasaki, southwest Japan, in the second arrest in the area in less than two months.

Japanese officers found some coral and tools to collect the organisms on the boat, but were yet to determine whether they were taken from Japanese territorial waters, the coastguard said.

The boat's captain Zhong Jinyin, 39, was taken to the coastguard's Nagasaki office while investigators inspected the boat, which had 10 other crew members on board, a spokesman said.

The coastguard approached the boat around 10:30 pm on Monday (1330 GMT) prompting the Chinese to flee, despite repeated Japanese orders to stop.

In total, five coastguard vessels took turns to chase the Chinese vessel until around 5 am, when the boat was stopped for an onboard inspection, the coastguard said.

"We used a speed boat to bring the boat's captain to (the coastguard's office in) Nagasaki. The onsite investigation of the vessel is continuing before we move the ship and the rest of the crew," a spokesman said.

"We are not experiencing any disobedient behaviour from the captain," he said.

The arrest came after a 42-year-old Chinese fisherman was charged last week with murder in South Korea over the fatal stabbing of a coastguard officer and the wounding of another as they tried to detain him and his boat for illegally operating in the Yellow Sea.

Arrests by Japan of straying Chinese fishermen are increasingly common and usually pass off without much of a hitch, but can occasionally spark international ructions.

In September 2010 relations between Tokyo and Beijing turned icy after a collision between a Japanese coastguard vessel and a Chinese fishing boat off disputed islands in the East China Sea.

Japan arrested the skipper near uninhabited -- but strategically coveted -- islands known in Japanese as Senkaku and in Chinese as Diayou, which both countries claim, but which are administered by Tokyo.

An irate China demanded his release, turning the screw with trade restrictions and the cancellation of diplomatic, political and cultural exchanges.

Japan eventually capitulated and released the fisherman, in what most observers saw as a victory for China in one of its key maritime disputes.

In early November Japan briefly held a Chinese fishing boat captain after his vessel was spotted in the same area of sea.

The 47-year-old skipper was arrested after a more-than four hour chase and detained for several days before paying a fine of around $3,900 and being allowed to go home.

China reacted calmly to the arrest and subsequent release, dubbing it "a normal fishery case" that was "properly settled".

The latest arrest comes as Japanese Prime Minister Yoshihiko Noda is due to visit Beijing for two days, starting Sunday.

China called on Japan to respect the legal rights of the fishermen.

"We have asked the Japanese side to ensure the safety of the Chinese crew and the boat and ensure their legitimate rights and interests," Chinese foreign ministry spokesman Liu Weimin told a regular daily press briefing.