Beijing has urged Japan's ambassador to stop the "illegal interception" of Chinese fishing boats.
Meanwhile, Japan has arrested the captain of the Chinese vessel.
The incidents in the East China Sea took place near a disputed chain of islands, which Japan controls but are claimed by both China and Taiwan.
According to state media the Chinese authorities told the Japanese ambassador that his country must stop what it called illegal interceptions of Chinese fishing boats.
A Japanese Coast Guard spokesman said the Chinese vessel had collided with two Japanese patrol boats in two separate incidents, 40 minutes apart. No injuries were reported.
She said the 41-year-old captain of the fishing boat had been arrested after repeatedly ignoring requests to leave the area.
A China's Foreign Ministry spokeswoman said China had repeated its claim to the Diaoyu islands and urged Japanese patrol boats in the area against any "so-called law enforcement activities or any actions that would jeopardise Chinese fishing boats or Chinese people".
The BBC's Martin Patience in Beijing says the collisions are the latest example of rising tensions between the two countries over territorial rights in the East China Sea.
The disputed chain of uninhabited islands which Japan controls are also claimed by China and Taiwan.
China calls them the Diaoyu islands while Japan refers to them as the Senkaku islands.
In the past Japan has lodged protests with China over entry of the country's vessels in to water close to this territory.
A diplomatic row has intensified between China and Japan after collisions between two Japanese patrol boats and a Chinese trawler on Tuesday.