China's top diplomat Wang Yi warned his Philippine counterpart that Manila "must act with caution", Beijing's foreign ministry said, following a flurry of tense maritime confrontations in the disputed South China Sea.

Wang said on a Wednesday call with Philippine Foreign Affairs Secretary Enrique Manalo that the two countries were "facing serious difficulties", blaming Manila for changing its policies, according to a readout.

"Wang Yi said China-Philippines relations are currently facing serious difficulties," it said.

"The root cause is that the Philippines has changed its longstanding policy stance, reneged on its own commitments, continued to provoke and stir trouble at sea, and undermined China's legal rights," it said.

"China-Philippines relations are at a crossroads. Faced with the choice of where to go, the Philippines must act with caution."

The Philippines summoned China's envoy on 11 December and flagged the possibility of expelling him following the most tense clashes between the countries' vessels in years at flashpoint reefs.

Videos released by the Philippine Coast Guard showed Chinese ships blasting water cannons at Philippine boats during two separate resupply missions to fishermen at Scarborough Shoal and a tiny garrison at Second Thomas Shoal the previous weekend. 

There was also a collision between Philippine and Chinese boats at Second Thomas Shoal, where a handful of Filipino troops were stationed on a grounded warship, with both countries trading blame.

China claims almost the entire South China 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 militarized to reinforce its claims.