The Philippines and China have agreed on an "arrangement" for resupplying Filipino troops stationed on a South China Sea reef, Manila said Sunday, after a series of escalatating confrontations in the disputed waters.

"The Philippines and the People's Republic of China have reached an understanding on the provisional arrangement for the resupply of daily necessities and rotation missions to the BRP Sierra Madre in Ayungin Shoal," the Philippine foreign ministry, using the Filipino name for Second Thomas Shoal.

A handful of Filipino troops are stationed on a rusty warship that was deliberately grounded on Second Thomas Shoal in 1999 to assert Manila's claims to the area.

It 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.

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

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