The Philippines foreign secretary, Albert Del Rosario, summoned the Chinese ambassador, Ma Keqing, to resolve the dangerous impasse diplomatically. Del Rosario's office said in a statement that the Scarborough Shoal "is an integral part of Philippine territory" and Filipino authorities would assert sovereignty over the offshore area.
The shoal lies off the north-west Philippine province of Zambales. China and the Philippines have been disputing ownership of the shoal, in addition to the Spratly Islands and other areas in the South China Sea.
Philippine foreign affairs spokesman Raul Hernandez said the situation at the shoal "has not changed as of this morning. There's a standoff."
The department of foreign affairs said on Sunday, a Philippine navy surveillance plane sighted eight Chinese fishing vessels anchored in a lagoon at Scarborough, prompting the military to deploy its largest warship, the BRP Gregorio del Pilar, which was recently acquired from the US.
On Tuesday, Filipino sailors from the warship boarded the Chinese vessels for an inspection, discovering large amounts of illegally collected corals, giant clams and live sharks inside the first boat, the department said in a statement.
Two Chinese maritime surveillance ships, identified as Zhonggou Haijian 75 and Zhonggou Haijian 84, later approached and positioned themselves between the Philippine warship and the Chinese fishing vessels, "thus preventing the arrests of the erring Chinese fishermen", the statement said.
Del Rosario protested to Ma, the Chinese ambassador in Manila, late on Tuesday and told her the Philippine navy would enforce Philippine laws, according to his office.
The Chinese embassy in Manila did not immediately comment. Chinese officials, who refer to Scarborough Shoal as Huangyan Island, have in the past asserted Chinese sovereignty over the area.
The Philippines refers to the shoal, a rich fishing ground, as Panatag.
Last year, the Philippines accused Chinese vessels of intruding into other parts of what it considers Philippine territory near the South China Sea, including the Spratlys. China has regularly dismissed the protests, saying Beijing has indisputable sovereignty over those areas on historical grounds.
The Spratly Islands south of Scarborough Shoal are claimed by China, the Philippines, Vietnam, Brunei, Malaysia and Taiwan. The chain of barren islands, reefs and coral outcrops are believed to be in rich in oil and gas and the overlapping claims have long been feared as Asia's next flashpoint for armed conflict.
The US, a defence-treaty ally of the Philippines, last year provided the Philippine navy with a refurbished coastguard cutter as part of efforts to shore up its naval defences.
Washington has insisted it takes no sides in the territorial dispute but says it should be solved peacefully. China has balked at what it considered a US interference in the region.
The disputes over the resource-rich Spratlys have settled into an uneasy standoff since the last major clash involving China and Vietnam, in which more than 70 Vietnamese sailors were killed in 1988.
Faced with China's formidable military, the Philippines and Vietnam have forged closer ties. Aside from military accords, the two countries agreed to set up a hotline between their coastguards and maritime police to monitor maritime incidents, such as piracy and incursions into their territorial waters.
The Philippine navy chief, Vice-Admiral Alexander Pama, said on Tuesday that Philippine and Vietnamese sailors agreed to play football and basketball matches in the islands they occupy in the Spratlys in a novel way to build trust in the contested region.
