The captain of a Chinese trawler which collided with Japanese patrol ships in waters off Diaoyu Islands was brought to a court on Ishigaki island in Okinawa Prefecture at around 14:00 p.m. (0500 GMT) Friday.
Japan Coast Guard arrested the captain for alleged "obstructing public duties" early Wednesday near the Diaoyu Islands in the East China Sea despite China's protest.
The other 14 crew members, all Chinese, were not arrested, but were kept in an area off Ishigaki.
The 41-year-old captain, Zhan Qixiong, was taken to Ishigaki branch of the Naha District Public Prosecutors Office on Thursday morning, according to Xinhua reporters at the scene.
On Tuesday, two Japan Coast Guard patrol boats and the Chinese fishing boat collided in waters off the Diaoyu Islands.
No injuries were reported, but the fishing boat was then intercepted by Japanese patrol boats.
China on Thursday said it opposes the way Japan was handling the Chinese fishing boat incident.
"China will never accept the Japanese side's applying domestic law to the Chinese fishing boat operating in that area," Chinese Foreign Ministry spokeswoman Jiang Yu told the regular briefing.
Jiang said Japan's handling was "absurd, illegal and invalid."