The announcement came at strategic talks in Washington yesterday, where the allies reiterated their opposition to the militarisation of outposts in those waters, where six Asian governments have competing claims.
China has built artificial islands with airstrips and military facilities as it asserts its claim to virtually all the South China Sea, including land features claimed by the Philippines.
Another of the five Philippine military bases where the US will have access is on southern Mindanao island, where the US is concerned about the presence of Muslim extremist groups.
Philip Goldberg, the US ambassador to the Philippines, said the pact would allow the US to rotate more forces and military assets through that country on a basis of mutual agreement with Manila. It can also conduct construction and position supplies, including for humanitarian relief.
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Goldberg said the US is not establishing its own bases as it had in the Philippines until 1992. They were closed amid a tide of Philippine nationalism.
Goldberg said he could not set a date for when US forces would be deployed but he expected movement of supplies and personnel to begin "very soon."
US Defence Undersecretary Pio Lorenzo Batino said the Philippines was a "reliable partner" and was looking forward to working with the US to develop the agreed-upon locations.
The implementation of the defence pact comes at a time of heightened tension in the South China Sea and will be opposed by China, which views the increased US presence in the region as an attempt at containment.