Incidents are the latest in a series of run-ins between Manila and Beijing in the disputed waterway.
The incidents occurred near Second Thomas Shoal in the Spratly Islands, where Beijing regularly deploys its vessels to assert its claims over almost the entire sea.
China’s coastguard said there had been a “slight collision” between one of its ships and a Philippine vessel carrying supplies to a World War II-era transport ship that was being used as an outpost on the shoal.
The coastguard said the collision occurred while it was “lawfully” blocking the boat from transporting “illegal construction materials” to the warship.
Manila said it condemned “in the strongest degree” the “dangerous blocking manoeuvres” of the Chinese vessel.
A Philippine coastguard vessel escorting the routine resupply mission was also “bumped” by a Chinese maritime militia vessel, Manila’s Task Force for the West Philippine Sea said.
However, China said the Philippine boat had “deliberately” stirred up trouble by reversing in a “premeditated manner” into a Chinese fishing vessel.
A video released by the Philippine military showed the Chinese coastguard ship’s bow and the stern of the resupply vessel touching briefly. It is not clear if the vessel suffered any damage.
The two countries have had numerous run-ins in areas of the South China Sea in recent months, especially the disputed Second Thomas Shoal, part of the Spratly Islands.
In August, China Coast Guard vessels used water cannon against a Philippine resupply mission preventing one of the boats from delivering its cargo.
Beijing claims sovereignty over almost the entire South China Sea, including parts of the exclusive economic zones of the Philippines, Vietnam, Malaysia, Brunei and Indonesia.
An arbitration panel in The Hague in 2016 ruled that China’s claims had no legal basis.
Beijing has rejected the ruling as “null and void” and having “no binding force”.