The incident happened during a Philippine mission to deliver provisions to a tiny garrison on Second Thomas Shoal, which is part of the Spratly Islands and a longstanding flashpoint between the countries.
China deploys coast guard and other vessels to patrol the hotly contested region and asserts its claim to almost the entire South China Sea.
Manila said the Chinese coast guard and other vessels "recklessly harassed, blocked, executed dangerous maneuvers" as they tried to "illegally impede or obstruct" Friday's mission.
A Chinese coast guard vessel had fired a water cannon against one of two supply boats, according to the Philippines' National Task Force for the West Philippine Sea.
The supply mission was also the target of "extremely reckless and dangerous harassment at close proximity" by Chinese boats inside the shoal, it said in a statement, adding that the Philippine vessels still managed to deliver their cargo.
China, however, said it "took control measures" against two Philippine transport boats and three coast guard vessels it insisted were in Chinese waters.
"The Philippines' actions infringe on China's territorial sovereignty," China Coast Guard spokesperson Gan Yu said.
"We urge the Philippines to immediately stop its infringing actions."
Second Thomas Shoal is about 200 kilometres (124 miles) from the western Philippine island of Palawan, and more than 1,000 kilometres from China's nearest major landmass, Hainan island.
A handful of Filipino troops are stationed on the crumbling BRP Sierra Madre, which the Philippine Navy grounded on the reef in 1999 to check China's advance in the waters.
The troops depend on the resupply missions for their survival.
The task force said the Philippine embassy in Beijing had lodged a protest with the Chinese foreign ministry over the latest incident, which it said had "put the lives of our people at risk".
"The systematic and consistent manner in which the People's Republic of China carries out these illegal and irresponsible actions puts into question and significant doubt the sincerity of its calls for peaceful dialogue," the statement said.
- 'They are not being deterred' -
Friday's incident comes nearly three weeks after two collisions between Chinese and Philippine vessels during another resupply mission to the BRP Sierra Madre, with the countries trading blame.
China's intentions were clearly designed to "stop the resupply missions to the Sierra Madre", said Jay Batongbacal, director of the University of the Philippines' Institute for Maritime Affairs and Law of the Sea.
"The use of water cannon again is an indication of something like renewed aggressive tendencies... it's like they are demonstrating that they are not being deterred by what we've been doing," he told AFP.
The Marcos administration has publicly criticised Chinese actions in the South China Sea, and sought stronger security ties with Japan and the United States in the face of Chinese actions in the waters.
Beijing has ignored a 2016 ruling by the Permanent Court of Arbitration in The Hague that its claims to almost the entire sea have no legal basis.
China has instead ramped up patrols of the waters and reefs in the South China Sea over the past decade or so and built artificial islands that it has militarised to reinforce its assertion.
The Philippines has outposts on nine reefs and islands in the Spratlys, including Second Thomas Shoal.
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