The Scarborough Shoal -- a triangular chain of reefs and rocks in the contested South China Sea -- has been a flashpoint between the countries since China seized it from the Philippines in 2012.

Monday's encounter took place "approximately 11.8 nautical miles southeast" of the Scarborough Shoal, the military said, during ongoing US-Philippine military exercises that Beijing has slammed as destabilising.

"The Chinese frigate BN 554 was documented tailing PS35 (BRP Emilio Jacinto) at close range, while BN 573 dangerously crossed its bow in a high-risk maneuver that created the danger of collision," the military said in a statement, labelling the incident "threatening and provocative".

China in response accused Manila of sending a ship to "intrude" into its territorial waters.

Its military said it had sent "naval and air forces to track, monitor, warn and drive away the Philippine boat in accordance with laws and regulations".

"The relevant remarks of the Philippines side disregarded the facts, confused the public, and attempted to mislead international cognition," said Colonel Tian Junli, spokesperson of the Chinese military's Southern Theater Command.

Philippines Rear Admiral Roy Vincent Trinidad told AFP the last such encounter between warships from the two navies he could remember was on a resupply mission in the South China Sea two years ago.

Alexander Lopez of Manila's National Maritime Council said the Chinese vessel had been "dangerously close" to its Philippine counterpart.

The ship crossing the bow of the BRP Emilio Jacinto had come within about 180 metres (590 feet), he told AFP, leaving "no room for any manoeuvre, for any emergency cases".

The Chinese vessel following alongside had been less than 100 metres away, he said.

China and the Philippines have engaged in months of confrontations in the South China Sea, which Beijing claims in nearly its entirety despite an international ruling its assertion has no merit.

A Filipino sailor lost a thumb last June when Chinese coast guard members wielding knives, sticks and an axe foiled a Philippine Navy attempt to resupply its troops stationed on the Second Thomas Shoal.

The joint US-Philippine exercises known as Balikatan, which this year were to simulate a "full-scale battle scenario", are set to end Friday.