Just days after taking office, the president [Obamaa] got word that the first strike under his administration had killed a number of innocent Pakistanis. “The president was very sharp on the thing, and said, ‘I want to know how this happened,’ “ a top White House adviser recounted.  In response to his concern, the C.I.A. downsized its munitions for more pinpoint strikes. In addition, the president tightened standards, aides say: If the agency did not have a “near certainty” that a strike would result in zero civilian deaths, Mr. Obama wanted to decide personally whether to go ahead.

The president’s directive reinforced the need for caution, counterterrorism officials said, but did not significantly change the program. In part, that is because “the protection of innocent life was always a critical consideration,” said Michael V. Hayden, the last C.I.A. director under President George W. Bush.  It is also because Mr. Obama embraced a disputed method for counting civilian casualties that did little to box him in. It 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.  Counterterrorism officials insist this approach is one of simple logic: people in an area of known terrorist activity, or found with a top Qaeda operative, are probably up to no good. “Al Qaeda is an insular, paranoid organization — innocent neighbors don’t hitchhike rides in the back of trucks headed for the border with guns and bombs,” said one official, who requested anonymity to speak about what is still a classified program.

This counting method may partly explain the official claims of extraordinarily low collateral deaths. In a speech last year Mr. Brennan, Mr. Obama’s trusted adviser, said that not a single noncombatant had been killed in a year of strikes. And in a recent interview, a senior administration official said that the number of civilians killed in drone strikes in Pakistan under Mr. Obama was in the “single digits” — and that independent counts of scores or hundreds of civilian deaths unwittingly draw on false propaganda claims by militants.

But in interviews, three former senior intelligence officials expressed disbelief that the number could be so low. The C.I.A. accounting has so troubled some administration officials outside the agency that they have brought their concerns to the White House. One called it “guilt by association” that has led to “deceptive” estimates of civilian casualties.  “It bothers me when they say there were seven guys, so they must all be militants,” the official said. “They count the corpses and they’re not really sure who they are.”

Excerpt, JO BECKER and SCOTT SHANE, Secret ‘Kill List’ Proves a Test of Obama’s Principles and Will, NY Times, May 29, 2012