It said a Chinese vessel at the Scarborough Shoal, in the Philippines' exclusive economic zone (EEZ), came within about seven metres of a Philippine fisheries boat on Friday, creating "a serious risk of collision".
"The PCG strongly condemns the dangerous and unprofessional actions of the China coast guard," spokesman Jay Tarriela said in a statement.
He said the shoal was a traditional fishing ground of Filipinos, "whose rights cannot be lawfully impeded by any foreign power".
Earlier on Friday, China's coast guard said it had imposed "control measures" on several Philippine vessels that it said were operating illegally in waters around Scarborough Shoal.
In a more detailed statement, the Chinese coast guard accused the Philippines of organising several government and coast guard vessels, along with a large number of fishing vessels, to "illegally gather" in the waters.
It said it had taken legal measures to warn, block and deploy water cannon after the official vessels from the Philippines ignored those measures from the coast guard and "insisted on intruding".
A similar incident took place on Thursday.
On Friday, China's foreign ministry said the coast guard's actions were "reasonable, lawful and beyond reproach".
"The Philippine side should immediately stop the infringement, provocation and hype," ministry spokesman Lin Jian said at a regular briefing.
China has long occupied the shoal, part of an armada of coast guard ships deployed throughout the South China Sea.
Beijing claims sovereignty over almost the entire waterway, including parts of the EEZs of Brunei, Indonesia, Malaysia, the Philippines, and Vietnam.
The incident came as Southeast Asian foreign ministers concluded regional meetings in Manila that were attended by Chinese Foreign Minister Wang Yi and US Secretary of State Marco Rubio, who called Beijing's actions in the South China Sea "disturbing" and reaffirmed support for defence treaty ally Philippines.
The two incidents at Scarborough Shoal, the South China Sea's most contested feature, followed a confrontation on Monday at the disputed Second Thomas Shoal, 650km away, where Manila said a Filipino sailor was injured after being struck with a baton by Chinese coast guard personnel.
China accused the Philippine navy of ignoring warnings and of trying to ram a Chinese patrol boat and the countries summoned each other's ambassadors in protest.
