President Benigno Aquino's spokesman Herminio Coloma said there was no timetable to complete the agreement which would allow more US troops and equipment access to the Philippines.
The agreement, which the two close allies have been discussing for several years, is seen as part of a Philippine effort to counter China's aggressive moves to back its claims to most of the South China Sea.
Asked by reporters if the accord would be completed before Obama's visit, Coloma said, "the government's priority is not with a timetable or with rushing something".
Coloma also hailed the just-concluded Philippine-US bilateral strategic dialogue in Washington where both sides expressed concern for "recent developments" in the South China Sea as well as the need to respect international law and freedom of navigation in those waters.
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Many observers believed the agreement would be completed ahead of Obama's visit to the Philippines as part of an Asian tour in April.
China claims virtually all of the South China Sea, a major shipping lane that is also a rich fishing ground and is believed to sit on vast mineral resources.
The Philippines along with Brunei, Malaysia, Taiwan and Vietnam all have competing claims to parts of the South China Sea.