The confrontation comes a week after China approved plans to turn the shoal into a national nature reserve, a move that defence analysts have warned would test Manila's response over the 150 sq km triangular chain of reefs and rocks.
The Philippine coast guard in turn accused its Chinese counterpart of harassing vessels it said were on a humanitarian mission to support fishermen.
Tuesday's encounter involved more than 10 Philippine ships, said Gan Yu, a spokesperson for China's Coast Guard, accusing the vessels of having "illegally invaded China's territorial waters of the Scarborough Shoal from different directions".
In particular, he faulted Philippine Coast Guard vessel 3014, saying in a statement it had "disregarded solemn warnings from the Chinese side and deliberately rammed a Chinese coast guard vessel".
He added: "The China coast guard lawfully implemented control measures against the Philippine ships."
These included measures such as verbal warnings, route restrictions and water cannon spraying, Gan added.
In a statement, the Philippine coast guard said it was engaged in a mission to resupply more than 35 Philippine fishing boats at the shoal when they encountered "aggressive actions" by nine Chinese vessels, and made no mention of water cannon.
Simmering tension over the shoal has led to diplomatic rows in recent years, but no incidents have escalated into armed conflict there.
Both sides accuse each other of provocations and trespassing in incidents featuring use of water cannon, boat-ramming and manoeuvres by China's Coast Guard the Philippines regards as dangerously close, as well as jets shadowing Philippine aircraft there.
A spokesperson for the Philippine Maritime Council said there was "no truth" in China's statement that it had taken control measures, which it dismissed as "another case of Chinese disinformation and propaganda".
Analysts have said Beijing's plan to categorise the shoal as a nature reserve amounted to trying to take the moral high ground in the dispute over the atoll, known as Huangyan Island in China and Panatag Shoal in the Philippines.
The dispute is part of a contest over sovereignty and fishing access in the South China Sea, a conduit for more than $US3 trillion of annual ship-borne commerce.
China claims almost the entire South China Sea, overlapping the exclusive economic zones of Brunei, Indonesia, Malaysia, the Philippines and Vietnam. Unresolved disputes have festered for years over ownership of various islands and features.
In 2016, the Permanent Court of Arbitration in the Hague ruled that China's sweeping claims in the region were not supported by international law, a decision that Beijing rejects.
with AP
