Beijing claims almost all of the economically vital body of water despite competing claims from other countries and an international court ruling that its assertion has no legal basis.
A Chinese coast guard spokesperson said Saturday's incident took place off the disputed Sabina Shoal, which has emerged as a new hotspot in the long-running maritime confrontations between the two countries.
Sabina Shoal is located 140 kilometres (86 miles) west of the Philippine island of Palawan and about 1,200 kilometres from Hainan island, the nearest major Chinese landmass.
Shortly after noon (0400 GMT), a Philippine ship "deliberately collided with" a Chinese vessel near the shoal, known in Chinese as Xianbin, China Coast Guard spokesperson Liu Dejun said, according to state broadcaster CCTV.
"China exercises indisputable sovereignty" in this zone, Liu said, condemning the "unprofessional and dangerous" conduct of the Philippine vessel.
However, Philippine Coast Guard spokesman Commodore Jay Tarriela said it was the China Coast Guard vessel 5205 that "directly and intentionally rammed" the Philippines' ship, BRP Teresa Magbanua.
The vessel has been anchored inside Sabina Shoal since April to assert Manila's claim over the area.
Tarriela said the BRP Teresa Magbanua was rammed three times -- hitting the port bow, starboard quarter and port beam.
No crew members were injured during the incident but the ship's bridge wing and freeboard were damaged. A hole was also found.
"It is important for us to take note that this ramming happened despite... our unprovoked action and presence in Escoda Shoal," Tarriela told reporters, using the Filipino name for Sabina Shoal.
The United States, a strong ally of Manila that had raised the South China Sea in high-level bilateral talks this week in Beijing, slammed China for "dangerous and escalatory" actions near Sabina Shoal.
Washington called on China to "comport its claims and actions with international law and to desist from dangerous and destabilising conduct", State Department spokesman Matthew Miller said in a statement.
- 'Serious concern' -
The collision was the fifth incident of Chinese maritime harassment this month, Tarriela said.
National Maritime Council Spokesperson Alexander Lopez said a report about the latest clash would be sent to the Philippine Department of Foreign Affairs for review and appropriate action.
"We take this with serious concern," Lopez told a news conference.
"We are there on a legal basis because that is ours, we don't need to ask for permission in our own territory. Let us be very clear about it," he said.
Philippine and Chinese vessels have collided near Sabina Shoal at least twice this month, and analysts say Beijing is trying to move deeper into Manila's exclusive economic zone and normalise Chinese control of the area.
The discovery this year of piles of crushed coral at the shoal ignited suspicion in Manila that Beijing was planning to build another permanent base there, which would be its closest outpost to the Philippine archipelago.
Recent clashes between Philippine and Chinese vessels have also taken place around Second Thomas Shoal in the Spratly Islands.
A Filipino sailor lost a thumb in a clash there in June when Chinese coast guard members wielding knives, sticks and an axe foiled a Philippine Navy attempt to resupply a small garrison.
Sabina Shoal is also the rendezvous point for Philippine resupply missions to the garrison on Second Thomas Shoal.
The repeated confrontations prompted Manila to brand Beijing the "biggest disruptor" to peace in Southeast Asia at a defence conference this month.
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