"The two sides discussed their respective positions on Ayungin Shoal and affirmed their commitment to de-escalate tensions without prejudice to their respective positions," the Philippine foreign ministry said in a statement, using the country's name for Second Thomas Shoal in the Spratly Islands.

Chinese coast guard personnel wielding knives, sticks and an axe surrounded and boarded three Philippine navy boats near the shoal last month, the latest and most serious in a number of escalating confrontations.

A Filipino soldier lost a finger in the June 17 clash, with Manila also accusing the Chinese coast guard of looting guns and damaging three boats as well as navigational and communication equipment.

Beijing insisted its coast guard behaved in a "professional and restrained" way and blamed Manila for the clash.

The Philippines foreign affairs undersecretary Theresa Lazaro and China's vice foreign minister Chen Xiaodong had "frank and constructive discussions", Tuesday's statement said.

"Noting recent incidents in the South China Sea, both sides recognized that there is a need to restore trust, rebuild confidence, and create conditions conducive to productive dialogue and interaction," the Philippine foreign ministry said, noting that "significant differences remain".

China claims almost the entirety of the South China Sea, brushing aside competing claims from several Southeast Asian nations, including the Philippines, and an international ruling that its stance has no legal basis.

Chinese forces have used water cannon and military-grade lasers and collided with Filipino resupply vessels and their escorts in previous confrontations.

The two sides signed an arrangement on improving the Philippines-China Maritime Communications Mechanism and agreed to continue discussions between their coast guards.

China and the Philippines launched the consultative meeting in 2017 to promote the peaceful management of conflicts in the South China Sea.

Philippine Foreign Affairs Secretary Enrique Manalo said last week the Manila meeting would look to establish "confidence-building measures" that can create the basis for "more serious discussions".

"We still believe in the primacy of dialogue, and diplomacy should prevail even in the face of these serious incidents, though I admit it's also a challenge," Manalo told a Philippine Senate public hearing on the Second Thomas Shoal confrontation.