Known in Chinese as the Ren'ai Reef, the shoal has seen an escalating number of confrontations between Chinese and Philippine ships in recent months as Beijing steps up efforts to push its claims to the disputed area.
These have often taken place during Philippine attempts to supply a garrison of Filipino troops on a grounded navy vessel, the Sierra Madre, which serves to assert Manila's claims to the reef.
The Second Thomas Shoal lies about 200 kilometres (120 miles) from the western Philippine island of Palawan and more than 1,000 kilometres from China's nearest major landmass, Hainan island.
The Chinese coast guard said that a Philippine resupply ship in the area had "ignored many solemn warnings from the Chinese side".
It "approached the... Chinese vessel in an unprofessional way, resulting in a collision", Beijing said, accusing the ship of having "illegally broken into the sea near Ren'ai Reef".
"The Chinese Coast Guard took control measures against the Philippine ship in accordance with the law," it added.
But the Philippine armed forces called China's version of events "misleading", decrying "the illegal presence and actions of Chinese vessels within the Philippines' exclusive economic zone".
Manila's national task force on the West Philippine Sea later said the Chinese vessels had "engaged in dangerous manoeuvres, including ramming and towing".
"Their actions put at risk the lives of our personnel and damaged our boats," it said.
Philippine Defence Secretary Gilberto C. Teodoro, meanwhile, vowed to defend his country's sovereignty, saying China's "dangerous and reckless behaviour in the West Philippine Sea shall be resisted".
"It should now be clear to the international community that China's actions are the true obstacles to peace and stability in the South China Sea," he added.
- Expansive claims -
Beijing claims almost the entirety of the South China Sea, brushing aside competing claims from several Southeast Asian nations including the Philippines and an international ruling that its stance has no legal basis.
It deploys coast guard and other boats to patrol the waters and has turned several reefs into militarised artificial islands.
It has in recent months stepped up moves against Philippine vessels in the area around Second Thomas Shoal.
This month, Manila accused Chinese boats of illegally seizing food and medicine airdropped to the Philippine outpost in the area.
It was the first time supplies had been seized, the military said.
Chinese personnel on the boats later dumped the items in the water, Philippine Navy spokesman for the West Philippine Sea Commodore Roy Vincent Trinidad said.
It was not clear if they belonged to the Chinese coast guard or navy, the military said.
China in response insisted the Sierra Madre was illegally grounded on the reef and urged the Philippines to "stop making trouble".
- 'Dangerous' incursions -
On Saturday, new Chinese coast guard rules took effect under which it can detain foreigners for alleged trespassing in the disputed sea.
The Philippines has accused the Chinese coast guard of "barbaric and inhumane behaviour" against its vessels, and President Ferdinand Marcos has called the new rules a "very worrisome" escalation.
China has defended its new coast guard rules. A foreign ministry spokesman said last month they were intended to "better uphold order at sea".
Chinese coast guard vessels have used water cannon against Philippine boats multiple times, and there have been collisions that injured Philippine troops.
The Group of Seven bloc on Friday criticised what it called "dangerous" incursions by China in the South China Sea.
Confrontations between China and the Philippines have raised fears of a wider conflict over the sea that could involve the United States and other allies.
Trillions of dollars in ship-borne trade passes through the South China Sea annually, and huge unexploited oil and gas deposits are believed to lie under its seabed, though estimates vary greatly.
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