"The Philippines protested the harassment, ramming, swarming, shadowing and blocking, dangerous manoeuvres, use of water cannons, and other aggressive actions of China Coast Guard and Chinese Maritime Militia vessels against" Filipino government vessels, it said in a statement.
Manila said it summoned Zhou Zhiyong, the number two official at the Chinese embassy in Manila, over the April 30 incident that damaged a Philippine Coast Guard (PCG) vessel and a Bureau of Fisheries and Aquatic Resources (BFAR) boat near the China-controlled Scarborough Shoal.
"China's aggressive actions, particularly its water cannon use, caused damage to vessels of PCG and BFAR. The Philippines demanded that Chinese vessels leave Bajo de Masinloc and its vicinity immediately," it said, using the Filipino name for the shoal.
The Chinese embassy did not immediately respond to requests for comment.
Manila and Beijing have a long history of territorial disputes in the South China Sea, with several collisions involving Philippine and Chinese vessels in recent months, as well as the use of water cannon by the China Coast Guard.
The latest incident happened near the China-controlled Scarborough Shoal, which has long been a potential flashpoint, during a mission to resupply Filipino fishermen.
On Tuesday, Chinese foreign ministry spokesman Lin Jian told reporters the China Coast Guard took "necessary measures" against Philippine vessels that infringed on Beijing's territory.
These measures were "in accordance with the law, and the way it handled the situation was professional," Lin said according to transcripts released by the Chinese embassy in Manila.
Tuesday's incident came as the Philippines and the United States held a major annual military exercise that has infuriated Beijing.