"These actions violated the International Regulations for Preventing Collisions at Sea (COLREGs) and endangered Filipino personnel engaged in a purely humanitarian undertaking," Philippine coast guard spokesperson Jay Tarriela said in a post on X on Thursday.
The incident happened as Southeast Asian foreign ministers gathered in Manila for ASEAN meetings that were also attended by Chinese Foreign Minister Wang Yi.
Earlier on Thursday, China said it tracked and drove away two Philippine vessels it accused of having "intruded into" waters near the disputed Scarborough Shoal despite warnings.
It was the second incident within days involving both nations in the South China Sea.
One of Asia's most contested maritime sites, Scarborough Shoal is claimed by both the Philippines and China, which calls it "Huangyan Dao".
"We urge the Philippines to immediately cease its infringing and provocative actions," China's Coast Guard said in a statement, while reaffirming China's sovereignty claims over the disputed shoal.
The Coast Guard took necessary measures, such as tracking, monitoring, and interception to drive away the Philippine vessels, it added, calling the actions "standard, professional and lawful".
The remarks came after protests by both sides this week following a clash between Beijing and Manila in the Second Thomas Shoal, another feature in the busy waterway of the South China Sea.
On the sidelines of an ASEAN meeting on Wednesday, the foreign ministers of both nations exchanged protests over the previous South China Sea encounter.
China's Wang warned Manila of "bitter consequences of its own making" if it sought to provoke Beijing with the support of outside powers.
