AFP journalists witnessed the incident from another Philippine boat less than a kilometre away.
The first vessel’s commanding officer said the Chinese ship came within 45m of his boat, and only quick actions avoided a collision.
The Chinese foreign ministry said Friday that the Philippine boats had “intruded” without China’s permission and called it a “premeditated and provocative action”.
Manila responded that “routine patrols in our own waters can be neither premeditated or provocative” and insisted the patrols would continue.
Marcos has said he will not let China trample on the Philippines’ rights in the sea, and has gravitated towards the US as he seeks to strengthen defence ties.
This month, the Philippines identified four military bases – in addition to five existing sites – to which US forces will have access, including one near the Spratly Islands.
The allies also carried out their largest-ever military manoeuvres in recent weeks.
This shift has alarmed China, which has accused Washington of trying to drive a wedge between Beijing and Manila.
US-Philippine ties were badly frayed under Marcos’s predecessor, Rodrigo Duterte.
Marcos has sought to allay public fears that the alliance with the US could bring the Philippines into a conflict if China were to invade Taiwan, which Beijing sees as its own territory to be reclaimed one day.
Marcos has said he will speak with Biden about the “need to tone down the rhetoric” over the South China Sea, Taiwan and North Korea.
White House Spokeswoman Karine Jean-Pierre said this month that Biden intended, in the meeting with Marcos, to “reaffirm the United States’ ironclad commitment to the defence of the Philippines”.
Before departing on Sunday, Marcos said he would convey to Biden that Manila wished to forge stronger ties in areas ranging from food and energy security, to “ensuring our resilience from threats to our economy, including global supply chain disruptions and economic coercion”.
Marcos added that he would push for “greater economic engagement” between the two countries and expected to meet US business leaders to promote trade and investment.