It said the mission to Second Thomas Shoal was the first since the Manila and Beijing reached a "provisional arrangement" earlier this month for the delivery of daily necessities and rotation missions for Filipino troops based on a rusty warship grounded atop the reef.

The shoal has been a focus of clashes between Chinese and Philippine ships in recent months as Beijing steps up efforts to push its claims to almost the entire South China Sea.

"No untoward incidents were reported" after a civilian vessel escorted by a Philippine Coast Guard boat reprovisioned the BRP Sierra Madre and rotated troops there on Saturday, a foreign department statement said.

The Chinese embassy did not immediately respond to requests for comment.

A Filipino sailor lost a thumb in the latest June 17 confrontation when Chinese coast guard members wielding knives, sticks and an axe foiled a Philippine Navy attempt to resupply its troops.

Following Manila's announcement of the arrangement, China's foreign ministry suggested it required the Philippines to give Beijing "prior notification" and verification of deliveries, which Manila promptly rejected.

Chinese Foreign Minister Wang Yi on Friday called on the Philippines to "honour its commitments" under the deal rather than "backtracking or creating complications", according to a readout of his meeting with Philippine foreign secretary Enrique Manalo at an ASEAN gathering in Laos.

Manalo said he hoped Beijing would keep its side of the bargain.

"If the parties implement, and we hope China implements the agreement, then we'll be able to resupply our military personnel on the ship without any obstruction," he said.

"I think that would be an important step forward in diffusing tensions and hopefully lead to other areas of cooperation on the South China Sea."

A handful of Filipino troops are stationed on the rusty Sierra Madre that was deliberately grounded on the shoal in 1999 to assert Manila's claims to the area.

They require frequent resupplies for food, water and other necessities as well as transport for personnel rotations.

The shoal lies about 200 kilometres (120 miles) from the western Philippine island of Palawan and more than 1,000 kilometres from China's nearest major landmass, Hainan island.