The Philippines slammed China's claims as "completely unfounded".
The two nations have had repeated confrontations in the waters in recent months, and on Saturday Manila accused China of twice firing flares at one of its patrol aircraft.
China has continued to press its claims to almost the entire sea, and has ignored an international tribunal ruling that its assertions have no legal basis.
Beijing accused the Philippine vessel of "deliberately" colliding with a Chinese Coast Guard ship.
It said the collision took place near the disputed Sabina Shoal, 140 kilometres (86 miles) west of the Philippine island of Palawan and about 1,200 kilometres from Hainan island, the closest Chinese landmass.
China Coast Guard spokesman Gan Yu said the collision occurred when a Philippine vessel refused to comply with "control measures" after attempting to deliver supplies to another vessel "illegally stationed" near Xianbin Reef in the Nansha Islands -- using the Chinese names for the Sabina Shoal and the Spratly Islands, also claimed by Manila.
"China warns the Philippines to immediately cease its infringing actions, otherwise the Philippines will bear all consequences resulting from this situation," Gan said.
The Philippines said that its ships encountered "aggressive and dangerous maneuvers" from the Chinese side when they were on a humanitarian mission to resupply Filipino fishermen with diesel, food and medical items.
The Chinese vessels "made close perilous maneuvers that resulted in ramming, blasted horns, and deployed water cannons", leading to an early termination of the resupply operation after their ship experienced engine failure, a statement from Manila's National Task Force on the West Philippine Sea said.
"These unprofessional, aggressive, and illegal actions posed serious risks to the safety of the Filipino crew and the fishermen they were meant to serve," the statement said, adding that no one was harmed.
Footage released by the Philippine Coast Guard showed a Chinese ship approaching and ramming the left side of its vessel.
Another clip showed a Chinese vessel travelling parallel to the Philippine ship, just metres away.
- Recurring clashes -
On Saturday the Philippines accused China of firing flares at one of its aircraft earlier this month as it patrolled the South China Sea.
On Monday both countries also reported a collision between their coast guard ships near Sabina Shoal.
Manila had said that was the first hostile action by Beijing against it near Sabina, where both sides have stationed coast guard vessels in recent months and where the Philippines fears China is about to build an artificial island.
US ambassador to the Philippines MaryKay Carlson, whose country has a mutual defence treaty with Manila, blasted the "unsafe, unlawful, and aggressive conduct" by the Chinese vessels on Sunday, saying it was "the latest in multiple dangerous actions" by China.
"We are steadfast in supporting" Philippine allies, she said on X.
China deploys boats to patrol the busy South China Sea and has built artificial islands that it has militarised to reinforce its claims.
In June, Chinese coast guard sailors brandished weapons including knives and an axe as they boarded Philippine naval vessels near the strategic reef.
The Philippine military said one of its sailors lost a thumb in the confrontation in which Beijing's coast guard also confiscated or destroyed Philippine equipment including guns.
Beijing blamed the escalation on Manila and maintains its actions to protect its claims are legal and proportional.
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