The judges quoted Obama in January 2012 saying, "I think that we have to be judicious in how we use drones. But understand that probably our ability to respect the sovereignty of other countries ... is enhanced by the fact that we are able to pinpoint-strike an al Qaeda operative in a place where the capacities of the military in that country may not be able to get them. So obviously a lot of these strikes have been ... going after al Qaeda suspects who are up in very tough terrain along the border between Afghanistan and Pakistan."

Between 2004 and 2013, Pakistani officials have estimated 2,200 people have been killed in that country alone from drone strikes, about 400 of them civilians. Other independent estimates have put the death total much higher. Pakistani officials have publicly condemned the use of unmanned aerial vehicles.

Before the U.S. court's ruling came out, United Nations counterterrorism investigator Ben Emmerson issued a statement Friday saying the American drone program "involves the use of force on the territory of another state without its consent, and is therefore a violation of Pakistan's sovereignty."

National security experts have said there are practical reasons for a policy of denial for covert programs.

"Covert actions are secret and they are deniable programs by the United States government, and if you talk about it publicly you begin to deny yourself the legal basis to use it as a covert action," said Fran Townsend, CNN national security contributor.

Practical, political reasons exits as well. Governments in Yemen and Pakistan want deniability of their own, to dampen any anti-American anger that might erupt over a classified program of killing operating within their borders.

The case is ACLU v. CIA (11-5320).