China claims almost the entire sea despite rival claims from other Southeast Asian countries including the Philippines, Vietnam and Malaysia.
Its coast guard and navy vessels routinely block or shadow Philippine ships patrolling the contested waters, Manila says.
The Philippine Coast Guard said the latest incident happened on June 30 during a regular operation to re-supply marines stationed in a run-down navy ship grounded at the Second Thomas Shoal to assert Manila's territorial claim in the waters.
As they neared the shoal, the two Philippine coast guard boats assigned as escorts for the navy mission were approached by two Chinese coast guard vessels.
One of the Chinese boats came within about 100 yards (90 metres) of the BRP Malabrigo's bow, forcing its commanding officer to slow down to avoid a collision, Commodore Jay Tarriela told reporters.
"They dangerously conducted different manoeuvres, even crossing the bow of the Philippine Coast Guard vessels and that kind of distance is very dangerous because that's already prone to collision," said Tarriela, the coast guard spokesman for the West Philippine Sea.
Manila refers to waters immediately to its west as the West Philippine Sea.
The Chinese embassy in Manila did not immediately respond to a request for comment.
A similar incident happened in April when a Chinese coast guard ship cut off the Philippine patrol vessel Malapascua as it carried journalists near the Second Thomas Shoal.
An AFP team was on another coast guard vessel and witnessed the near collision.
In that incident, the Malapascua's commanding officer Rodel Hernandez said the Chinese ship came within 45 metres of his boat and only his quick actions avoided the steel-hulled vessels crashing into each other.
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