Japan released a Chinese fishing boat captain on Wednesday after he paid a fine of reportedly around $3,900 for entering Japanese waters, in the latest maritime incident between the two sides.

The episode occurred on Sunday, when a Japanese coastguard patrol boat spotted two Chinese fishing boats in Japanese waters and gave chase when the vessels refused to stop for an on-board inspection.

The 47-year-old captain of one of the fishing boats was arrested after a four-and-a-half-hour chase and was detained along with 10 crew members. The patrol boat rammed the vessel to stop it getting away.

"This is a normal fishery case and has been properly settled," Chinese foreign ministry spokesman Hong Lei told a regular briefing in Beijing.

"After paying the fines, the Chinese ship captain and 10 Chinese fishermen detained by the Japanese side have been released and are now on their way back home."

Local prosecutors filed a summary indictment against the fisherman for violating Japan's fisheries law, with the Nagasaki summary court ordering him to pay a fine of 300,000 yen ($3,900), Jiji Press said.

The local prosecutors' office in Nagasaki declined to confirm the report.

China and Japan have often had tense ties, particularly over disputed islands in the East China Sea known as Senkaku in Japan and Diaoyu in China.

But the latest incident occurred in Japanese waters off southwestern Nagasaki, not near the disputed waters.

Beijing's comment that the arrest of the Chinese fishing boat captain was a "regular fishery case", is an indication the incident would not affect ties between the two Asian rivals.

The measured comments contrasted markedly with China's furious reaction to another maritime incident in September 2010, when Japan arrested a Chinese trawler captain that rammed two coastguard patrol boats near disputed islands.

China issued protests and scrapped meetings and cultural events in a diplomatic offensive that continued after Japan freed the captain, while nationalist sentiment sparked demonstrations in both countries.