Beijing urged Tokyo on Friday to protect the rights of a Chinese crew after a fishing boat was seized by Japanese authorities.

"It is hoped Japan strictly respects the China-Japan fisheries agreement, fairly enforces the law and safeguards the safety and legitimate rights and interests of Chinese crew members," Foreign Ministry spokesman Lin Jian said on Friday.

The seizure of the Chinese fishing vessel happened on Thursday off southern Japan.

Japan's fisheries agency said the vessel's captain was ordered to stop for an inspection, but the boat "failed to comply and fled".

"Consequently, the vessel's captain was arrested on the same day," the agency said in a statement.

Japanese authorities said the boat was inside Japan's exclusive economic zone, some 166 kilometres south-southwest of Meshima Island in the Goto Archipelago.

The captain was named as Zheng Nianli.

The status of the other 10 people on board the vessel, named the Qiong Dong Yu, was unclear. (AFP)