But Philippine President Ferdinand Marcos hit back later Thursday, vowing not to succumb to "coercion", insisting recent tense stand-offs in the disputed area highlighted his nation's "courage".
Videos released by the Philippine Coast Guard showed Chinese ships blasting water at Philippine boats this month, and there was also a collision between vessels from the two countries during tense clashes at flashpoint reefs.
China's top diplomat warned his Philippine counterpart this week that the two countries were "facing serious difficulties" and blamed Manila, a readout late Wednesday showed.
"The root cause is that the Philippines has changed its policy stance so far, reneged on its own commitments, constantly provoked troubles at sea and undermined China's legitimate and lawful rights," the statement said.
"China-Philippines relations are at a crossroads. Faced with the choice of where to go, the Philippines must act with caution," it continued.
On Thursday, Chinese foreign ministry spokesman Wang Wenbin reiterated his country's warning and added that Beijing hoped the Philippines "can make a rational choice... and work with China to properly handle and manage the current maritime situation".
Philippine Foreign Minister Enrique Manalo described the call with Wang Yi as "frank and candid", according to a readout released by the Philippines foreign ministry on Thursday.
"We... ended our call with a clearer understanding of our respective positions on a number of issues," the readout quoted Manalo as saying, noting the "importance of dialogue in addressing these issues".
But later on Thursday Marcos, speaking to troops at a celebration marking the 88th anniversary of the Philippine military, was defiant.
He did not mention China by name, but made clear reference to the recent confrontations, calling them "worrisome".
"We shall continue to assert our rights in accordance with the Philippine constitution and international law," he said.
"(The recent incidents are) a proud demonstration of Filipino courage against coercion and our firm resolve to protect, preserve and uphold our territorial integrity," he said to applause.
- Envoy summoned -
Relations between Manila and Beijing have frayed under Marcos, who has sought to improve ties with traditional ally Washington and deepen defence cooperation in the region, while also pushing back against Chinese actions in the South China Sea.
Beijing 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.
The Philippines summoned China's envoy on December 11 and flagged the possibility of expelling him following the latest clashes.
The videos released by the Philippines were of incidents 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 are stationed on a grounded warship, with both countries trading blame.
Marcos met Chinese leader Xi Jinping last month on the sidelines of an Asia-Pacific summit in San Francisco, where the pair discussed the maritime territorial disputes.
Marcos later told a forum in Hawaii the Philippines would not give up "a single square inch of our territory".
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