Foreign Affairs Secretary Teodoro Locsin said no one was hurt during the Nov 16 incident at the Second Thomas Shoal but the Philippines boats, which were transporting food supplies to military personnel based there had to abort their mission.
"The acts of the Chinese Coast Guard are illegal," Locsin said in a statement, reminding China that a public vessel is covered by the Philippines-United States Mutual Defense Treaty.
Locsin said he had conveyed "in the strongest terms" to the Chinese Ambassador to Manila "our outrage, condemnation and protest of the incident."
Locsin warned Beijing's "failure to exercise self restraint threatens the special relationship" between the two countries.
"China has no law enforcement rights in and around these areas. They must take heed and back off," Locsin said.
Manila regards Second Thomas Shoal, which lies 105 nautical miles (195 km) southwest of the Philippine region of Palawan, as being within its 200-nautical mile exclusive economic zone. It has occupied the shoal since 1999 after intentionally grounding a navy ship on the reef.
China, which claims virtually all the South China Sea, says the reef is part of its territory, but a 2016 ruling by Permanent Court of Arbitration in The Hague found in favour of the Philippines.
The Chinese embassy in Manila did not immediately respond to requests for comment from the media.
China claims sovereignty over vast swathes of the South China Sea, but Brunei, Malaysia, the Philippines, Taiwan and Vietnam also have lodged competing claims for some or all of the islands.