US forces will gain access to more military bases in the Philippines than the five already announced, US Defence Secretary Ashton Carter said Wednesday as he began a visit to the longstanding Asian ally.

Manila announced this year it would allow US forces to use five of its installations, including an air base close to the South China Sea.

The agreement that went in force in January aims to strengthen the Philippines' defensive capabilities amid a tense maritime dispute with China, while helping the Pentagon pivot more of its forces toward Asia.

"They will be more, these are just the five initial sites for rotational presence" of US troops, Carter told reporters on his flight to the Philippine capital from India.

"The agreement provides for more sites in the future," he said.

Short-term rotations of US forces and equipment through these five facilities is "our favourite way of having a presence, for US forces to operate in and out of the Philippines, in support of our allies, of our broader networks of friends and allies in the region."

Carter is in Manila to attend Friday's ceremony marking the end of an annual large-scale joint military exercise between the two allies.

He is scheduled to call on President Benigno Aquino on Thursday.

Carter said he did not know at this time how many more Philippine military bases would be opened to US use.

"This is an evolving thing. We agreed to do these five with an understanding that they could be more and would be more, as we see what else and where else is significant," he added.

The five already approved by Manila include the Antonio Bautista air base on the western Philippine island of Palawan.

The base is just 300 kilometres (186 miles) east of Mischief Reef, an outcrop occupied by China in the 1990s despite angry protests by the Philippines.

China claims virtually all the strategic and resources-rich South China Sea despite conflicting partial claims by Brunei, Malaysia, Vietnam, Taiwan and the Philippines.

Beijing has in recent months been asserting its claim by occupying more reefs and outcrops in these waters, and building artificial islands including airstrips on some of them.

The Philippines has warned the Chinese activity could be a prelude to Beijing declaring an air defence zone in the area.

Washington does not take sides in the territorial disputes, but has warned against attempts to disrupt freedom of navigation in international waters.

Under the accord, US forces will also gain access to Basa air base, about 330 kilometres from Scarborough Shoal which was occupied by Chinese vessels after a tense confrontation with Philippine ships in 2012.

The other bases to be used by the US military are a major army training camp with its own airstrip in the north, and two air bases in the central and southern islands of the archipelago.