China's coast guard on Sunday took "control measures" after a Philippine vessel entered waters near a disputed shoal in the South China Sea, Beijing's state media said.

"The Philippine vessel 3002 illegally intruded into the waters near Xianbin Reef in the Nansha Islands without permission from the Chinese government," state broadcaster CCTV said, using the Chinese names for the Sabina Shoal and the Spratly Islands.

The vessel then "continued to dangerously approach a Chinese coast guard vessel conducting normal operations", CCTV said, adding that the coast guard had "taken control measures against the Philippine vessel in accordance with the law and regulations". 

The Philippines a day earlier accused China of recently firing flares at one of its aircraft as it patrolled over the South China Sea. 

And on Monday, both countries said their coast guard ships had collided near the disputed Sabina Shoal, located 140 kilometres (86 miles) west of the Philippine island of Palawan and about 1,200 kilometres from Hainan island, the closest Chinese landmass.

Manila had said that it was the first hostile action by Beijing against it near Sabina, where both sides have stationed coast guard vessels in recent months and where the Philippines fears China is about to build an artificial island.

China and the Philippines have had repeated confrontations in the waters in recent months, including around a warship grounded years ago by Manila on the contested Second Thomas Shoal that hosts a garrison.

China claims almost the entire sea and has ignored an international tribunal ruling that its assertions have no legal basis. 

It deploys boats to patrol the busy waterway and has built artificial islands that it has militarised to reinforce its claims.