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 the fishing operation law 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.