But the Times reports some of those strikes are made without positive, concrete confirmation of the identities of those in the strike zone. These so-called "signature strikes" hit targets based on evidence of suspicious behavior. Who is on the ground at the time is often unknown.
According to the Times, the method "in effect counts all military-age males in a strike zone as combatants, according to several administration officials, unless there is explicit intelligence posthumously proving them innocent."
Human rights advocates called the approach alarming, making it difficult to determine whether and how many noncombatants might have been killed. The policy, they say, highlights the lack of transparency and accountability for the administration's secret drone program.
"Americans were disturbed when information came to light about a secret policy of torture. And we should be even more disturbed about a secret policy of killing," Hina Shamsi, director of the national security project at the ACLU, told ABC News.
"There's something very wrong with a program that assumes guilt by association as permissible basis for killing," said Shamsi.
Andrea Prasow, senior counterterrorism counsel at Human Rights Watch, tells ABC News: "The most troubling part of the report for me is the idea that the only way an innocent person is counted as an innocent victim is if -- posthumously -- they manage to make their case. It's a little hard to do that.
"We have official government statements that hardly anyone was the erroneous victim of a drone strike, with private calculations in the hundreds if not thousands. The number probably falls somewhere in the middle," she said. "But we will never know for sure."
Both groups have protested the CIA's secret drone program calling it unlawful and dangerous, and saying it unduly imperils innocent lives and the security of the U.S. Some say it sets a precedent that other countries like China or Russia might cite in targeting their own alleged enemies of the state.
"As the drone campaign wears on, hatred of America is increasing in Pakistan. American officials may praise the precision of the drone attacks, but in Pakistan, news media accounts of heavy civilian casualties are widely believed," wrote Dennis Blair, former Director of National Intelligence in a New York Times op-ed late last year. "Our reliance on high-tech strikes that pose no risk for our soldiers is bitterly resented in a country that cannot duplicate such feats of warfare without cost to its own troops."
But top Obama administration officials believe the strikes are an effective way to keep Americans safe at home, a top priority no matter the cost.
"I think this is one of the most precise weapons that we have in our arsenal. Number two, what is our responsibility here? Our responsibility is to defend and protect the United States of America," Defense Secretary Leon Panetta told ABC News' "This Week."