China has warned the Philippines that it "must act with caution", Beijing's foreign ministry said, following a string of incidents in the disputed South China Sea as Manila increasingly stands up to Chinese assertiveness in the region.

Videos released by the Philippine Coast Guard showed Chinese ships blasting water cannon at Philippine boats this month and there was also a collision between vessels from the two countries during tense clashes at flashpoint reefs.

Wang Yi, China's top diplomat, said on a call with Philippine Foreign Affairs Secretary Enrique Manalo on Wednesday 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 late on Wednesday.

"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."

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

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 militarised to reinforce its claims.

Manalo described his call with Wang as "frank and candid", according to a readout released by the Philippines foreign ministry on Thursday.

"We had a frank and candid exchange and ended our call with a clearer understanding of our respective positions on a number of issues," the readout quoted Manalo as saying.

"We both noted the importance of dialogue in addressing these issues."

Envoy summoned