The Philippines have accused China of using water cannons at a supply vessel, damaging part of the ship.
Officials in Manila have claimed the supply vessel, which was on a routine resupply mission in the South China Sea was targeted by two Chinese Coast Guard vessels.
The Philippines' task force on the South China Sea said the water cannon incident shattered the supply boat's windshield and caused minor injuries to its crew.
It also accused China of conducting "dangerous manoeuvres" which led to a collision between the Philippine and the Chinese coastguard vessels.
Manila's South China Sea task force said Philippine vessels carrying out the routine mission to the Second Thomas Shoal were "harassed (and) blocked" by Chinese maritime militia and coast guard ships earlier today .
Chinese coast guard ships fired the water cannon, shattering the windshield of one of the resupply boats and causing minor injuries to at least four crew members.
China's coastguard said the Philippine vessels illegally intruded into its waters. Beijing claims sovereignty over most of the South China Sea, a claim that cuts into the exclusive economic zones (EEZ) of Vietnam, the Philippines, Malaysia, Brunei and Indonesia.
The Permanent Court of Arbitration in 2016 found China's claims had no legal basis.
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The Philippine foreign ministry said it had summoned the Chinese diplomat to convey its protest and to demand that Chinese vessels immediately leave the vicinity of the Second Thomas Shoal, which Manila calls Ayungin.
A spokesperson from the ministry said: "China's interference with the Philippines' routine and lawful activities in its own exclusive economic zone is unacceptable. China's actions in Ayungin Shoal infringes upon the Philippines' sovereign rights and jurisdiction."
China laid the blame on Manila, saying Philippine ships had illegally intruded into waters adjacent to the Second Thomas Shoal, which it calls Renai Reef, so it had to take control measures.
United States ambassador to the Philippines MaryKay Carlson said: "The US stands with the Philippines and proponents of international law in support of a #FreeAndOpenIndoPacific."
China claims almost the entire South China Sea, which includes the Second Thomas Shoal, and has deployed vessels to patrol the disputed atoll which lies within the Philippines' EEZ.
The most recent incident was the latest in a series of maritime run-ins between the Philippines and China, which have been locked in a territorial dispute in the South China Sea.
This is despite a 2016 ruling by the Permanent Court of Arbitration which found that China's claims had no legal basis. Beijing rejects that ruling.
The Philippine task force said Beijing's "unprovoked acts of coercion and dangerous manoeuvres" put "into question the sincerity of its calls for peaceful dialogue and lessening of tensions."
Chinese Foreign Ministry spokesperson Mao Ning told a press conference in Beijing the operation was "professional and restrained, reasonable and lawful."
