In September, Obama ordered his administration to prepare to accept at least 10,000 refugees fleeing the war in Syria.
Obama says the US has an "ironclad" commitment to security in the Philippines.
CIA director John Brennan says Paris attacks were carefully planned over a course of several months.
The Stars and Stripes will also be flown at half-staff at all US embassies and missions overseas.
The prisoners could not be sent to their homeland because the US considers Yemen too unstable to accept prisoners from Guantanamo.