A coast guard vessel and another government boat were damaged in the April 30 incident near the disputed Scarborough Shoal, according to the Philippines' foreign ministry.
Manila and Beijing have a long history of territorial disputes in the South China Sea, and the neighbours have been involved in several maritime incidents in recent months as they assert their rival claims in the strategic waterway.
The latest, near the China-controlled Scarborough Shoal, occurred during a mission to resupply Filipino fishermen.
Zhou Zhiyong, the number two official at the Chinese embassy, was summoned by Manila over "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", according to a statement from the foreign ministry.
"China's aggressive actions, particularly its water cannon use, caused damage" to the Philippines' vessels, the ministry added, demanding that the Chinese boats immediately leave the shoal and its vicinity.
The Philippines said the pressure in Tuesday's water cannon incident was far more powerful than anything previously used, and that it tore or bent metal sections and equipment on the Philippine vessels.
Thursday's diplomatic protest was the 20th lodged by Manila this year, and 153rd since President Ferdinand Marcos came to power in mid-2022, the foreign ministry said.
The Chinese embassy did not immediately respond to a request for comment.
China's coast guard had previously said it "expelled" the two Philippine ships from its waters near Huangyan Island, the Chinese name for Scarborough Shoal.
The shoal has been a flashpoint between the two countries since China seized it from the Philippines in 2012.
- Major military exercise -
China claims almost the entire South China Sea, brushing off rival claims from other countries, including the Philippines, and an international ruling that its assertion has no legal basis.
The triangular chain of reefs and rocks that make up Scarborough Shoal lies 240 kilometres (150 miles) west of the Philippines' main island of Luzon and nearly 900 kilometres from Hainan, the nearest major Chinese land mass.
Since seizing the shoal, Beijing has deployed its coast guard and other vessels that Manila says harass Philippine ships and prevent its fishermen from accessing the rich lagoon.
The latest incident came as the Philippines and the United States held a major annual military exercise that has infuriated Beijing.
Manila and Washington have a mutual defence treaty and recent confrontations between Philippine and Chinese vessels have fuelled speculation of what would trigger it.
President Marcos said last month that US Defense Secretary Lloyd Austin had given assurances that the treaty would be invoked if another "foreign power" killed a Filipino soldier.
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