The US Army said in April it had deployed the Mid-Range Capability missile system which can fire the Standard Missile 6 (SM-6) and the Tomahawk Land Attack Missile in the northern Philippines.

Philippine troops have been taught how to use and maintain the Typhon missile system, but it was not used in live-fire exercises, Colonel Louie Dema-ala told AFP.

"As per plan... it will be shipped out of the country in September or even earlier," Dema-ala said.

"The US Army is currently shipping out their equipment that we used during Balikatan and Salaknib (exercises)." 

The presence of the mid-range missile system on Philippine soil had angered Beijing. 

Chinese Defence Minister Dong Jun warned in June there were "limits" to Beijing's restraint on the South China Sea and over the deployment of ballistic missiles in the Asia-Pacific region.

Dong's remarks at a security forum in Singapore were a clear reference to the Philippines and the United States, which have been boosting defence ties in the face of China's growing military might and influence.

The deployment of "medium-range ballistic missiles" was "severely damaging regional security and stability", Dong said.

"Acting in this way will ultimately burn oneself."

Earlier on Tuesday, the Philippines and China agreed on the need to "restore trust" and "rebuild confidence" to better manage maritime disputes, even as Manila told its neighbour it will be "relentless" in protecting its interests in the South China Sea.

The Philippine foreign ministry said it had "frank and constructive" discussions with China on the South China Sea during the ninth round of talks under their Bilateral Consultation Mechanism, hosted by Manila.

The high-level meeting between senior foreign ministry officials followed what the Philippine military described as the "most aggressive" actions in recent history by China's Coast Guard against its vessels during last month's routine resupply mission that seriously injured a Filipino sailor. 

"There was substantial progress on developing measures to manage the situation at sea, but significant differences remain," the Department of Foreign Affairs (DFA) said in a statement.

Earlier in the day, the Vatican's foreign minister Archbishop Paul Richard Gallagher, called for the peaceful resolution of conflicts, including in the South China Sea, which China mostly claims as its own territory.

"We encourage parties in conflict to abide by international law," Gallagher, who is in Manila for an official visit, said in a joint press briefing with his Philippine counterpart. 

Manila has sought wider international support on its maritime claims, seeking closer ties with countries to advocate for a rules-based order that recognises international law.