The move provoked a warning from the Philippine government that its vessels are covered under a mutual defence treaty with the United States.
Philippine Foreign Secretary Teodoro Locsin said no one was hurt in the incident on Tuesday, but the two supply ships had to abort their mission to provide food supplies to Filipino forces occupying the Second Thomas Shoal, which lies off western Palawan province in the Philippines' internationally recognised exclusive economic zone.
Locsin said in a tweet the three Chinese coastguard ships' actions were illegal and he urged them "to take heed and back off".
His government has conveyed to China "our outrage, condemnation and protest of the incident", Locsin said, adding "this failure to exercise self-restraint threatens the special relationship between the Philippines and China" that President Rodrigo Duterte and his Chinese counterpart Xi Jinping have worked hard to nurture.
There was no immediate comment from Chinese officials in Manila or Beijing.
The incident is the latest flare-up in the long-simmering territorial disputes in the strategic waterway, where China, the Philippines, Vietnam, Malaysia, Brunei and Taiwan have overlapping claims.
China claims virtually the entire waterway and has transformed seven disputed shoals into missile-protected island bases, ratcheting up tensions.
National Security Adviser Hermogenes Esperon told reporters in Manila the government will deploy coastguard and Bureau of Fisheries vessels instead of navy ships to back up Filipino forces and enforce Philippine fishing laws at Second Thomas Shoal, which Filipinos call Ayungin and China refers to as the Ren'ai reef.
The number of Chinese surveillance ships has increased in recent weeks in the far-flung atoll and also around Thitu, a larger Philippine-occupied island in the Spratly archipelago in the South China Sea's most hotly contested area, he said.
"We will continue the resupply and we do not have to ask the permission of anybody because that is within our territory," Esperon said.
The Philippine military deliberately ran aground a World War II-era warship, the BRP Sierra Madre, at the submerged atoll in 1999 to fortify its claim and provide a shelter to a small contingent of Filipino marines.
The Sierra Madre is now effectively a rusty shipwreck but the Philippine military has not decommissioned it. That makes the ship an extension of the government and means any attack on the ship is tantamount to an assault against the Philippines.
Washington has no claims in the busy waterway but has patrolled the region with its navy ships and aircraft to assure its allies, including the Philippines, and ensure freedom of navigation and overflight.
China has repeatedly warned the US to stay away from the disputed waters and not meddle in what it says is a regional issue.
