The boat was loaded with more than 350 endangered turtles that were confiscated when it was seized near territory known as Half Moon Shoal, Philippine maritime police Chief Superintendent Noel Vargas said.
China demanded that the Philippines release the boat, and Foreign Ministry spokeswoman Hua Chunying urged Manila to "stop taking further provocative actions."
China earlier said via state media that Chinese officials lost contact with 11 fishermen after they were intercepted by armed men near Half Moon Shoal not far from the Philippines.
China lays claim to virtually the entire South China Sea and is locked in an increasingly heated dispute with the Philippines, Vietnam and others over rights to energy resources, fishing grounds and island outposts.
Vargas said the Chinese boat will be taken to the western Philippine province of Palawan, about 110 kilometres from Half Moon Shoal, and the fishermen will face charges of violating Philippine laws prohibiting catches of endangered green sea turtles.
China's official Xinhua News Agency said the Chinese fishermen's vessel was intercepted yesterday by armed men who fired warning shots in the air. An official from the Fishing Port Monitoring Centre at Tanmen in China's Hainan province confirmed the report. He said he had no other details and declined to give his name, as is common among Chinese bureaucrats.
