But the tense situation is not yet resolved, as a Philippine coast guard boat remains at the scene, and a third Chinese ship has arrived, said Raul Hernandez, a spokesman for the Philippine Department of Foreign Affairs.
The Philippine naval vessel -- the BRP Gregorio del Pilar, a 378-foot cutter -- has moved away from the lagoon for "reprovisioning" and a decision has not yet been announced on whether it will return, Hernandez said.
He said negotiations were continuing with the Chinese in the hope of finding a "diplomatic solution" to the impasse at Scarborough Shoal, which both countries claim is "an integral part" of their territory. Scarborough Shoal is about 200 kilometers west of the Philippine mainland.
"For now, the ball is on the side of the Chinese," Hernandez said.
The Philippines sent the Gregorio del Pilar to the area of Scarborough Shoal on Sunday after surveillance aircraft spotted eight Chinese fishing boats anchored inside the lagoon.
A boarding team from the Gregorio del Pilar went to inspect the Chinese fishing boats Tuesday morning and found "large amounts of illegally collected corals, giant clams and live sharks" inside one of the boats, according to the Philippine government.
Later Tuesday, the Gregorio del Pilar reported that the two Chinese surveillance ships had arrived and taken up a position at the mouth of the lagoon, blocking the way to the fishing boats and "preventing the arrest" of the fishermen.
The Philippines said Thursday that it had sent the coast guard vessel to support the Gregorio del Pilar. It also reported the arrival of the third Chinese vessel, which it said was from China's Bureau of Fisheries.
The Chinese Embassy in Manila has complained to the Philippine authorities about "the harassment of Chinese fishermen," China's official news agency, Xinhua, reported Wednesday.
China has "urged the Philippine side to stop immediately their illegal activities and leave the area," Xinhua reported, saying that the fishermen were taking shelter in the lagoon "due to harsh weather conditions."
The embassy is "engaged in discussions with the Philippine Department of Foreign Affairs to seek a solution" and maintain peace and stability in the South China Sea, Xinhua said.
The South China Sea -- a 1.3 million square mile patch of the Pacific Ocean bracketed by China and several Southeast Asian nations -- is dotted with hundreds of largely uninhabited islands and coral atolls that are home to some of the world's most diverse marine life. Also under its waves lie potentially huge reserves of natural gas and oil.
That prospect has peppered the sea with competing claims from China, Vietnam, the Philippines, Malaysia, Brunei and Taiwan. It has also resulted in frequent small-scale clashes. Last year, a spate of incidents took place between Chinese and Vietnamese vessels.
