White House counterterrorism adviser John Brennan on Monday spoke openly -- and at great length -- about what has long been one of the government’s most controversial official secrets:  the use of remotely piloted drones to kill suspected terrorists.

In doing so, he became the first U.S. government official to acknowledge that the drone strikes sometimes kill innocent people, though he characterized such deaths as  “exceedingly rare.” But a new analysis by an independent Washington think tank estimates that more than 300 civilians have been killed by drones since President Barack Obama took office.

In a major speech on the anniversary of Osama bin Laden’s death during a raid in Abbottabad, Pakistan, by U.S. Navy SEALs, Brennan proclaimed that al-Qaida is now "on the path to its destruction."  But the headline was what he had to say about the drone program — long a forbidden subject for senior U.S. officials  — and how the U.S. government uses it.

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“The United States conducts targeted strikes against specific al-Qaida terrorists, sometimes using remotely piloted aircraft, often referred to publicly as drones,” said Brennan, in his speech at the Woodrow Wilson International Center for Scholars, a Washington, D.C., foreign policy think tank.  

While it has been openly reported in the press for years, the use by the CIA of pilotless drones to kill members of al-Qaida has long been officially classified,  prompting government officials to talk obliquely about “lethal operations” and “removal” of terrorists. They have done so even as Obama has dramatically escalated the number of such attacks and made them the central component of the administration’s counterterrorism efforts.

One U.S. intelligence official, speaking on condition of anonymity, told NBC News that the speech represents “a pretty big sea change for us” in terms of what officials will now be permitted to talk about. But the official said that while Brennan’s speech had been carefully vetted throughout the U.S. intelligence and national security community, there had been no formal declassification of the drone program. “The president can declassify anything he wants,” said the official, adding that Brennan – as the representative of the president — can speak about anything his boss wants him to discuss.   

Under Obama, there have been an estimated 250 drone strikes in northwest Pakistan that have killed as many as 2,345 people, according to an analysis by the New America Foundation, a Washington think tank that closely tracks the program. Such strikes have generated a storm of protest in Pakistan and stepped up demands by the Pakistani government to halt them.   

In what he described as an effort to be more open with the American people, Brennan on Monday described an elaborate process under which senior government officials select targets for drone strikes. They must first determine whether a prospective target is a bona fide member of al-Qaida or “associated forces” and poses a “significant threat” to U.S. interests.  The “lethal action” strikes are not used for “punishing terrorists for past crimes” or “seeking vengeance.” Instead, they are used to “stop plots” and “prevent future attacks,” citing as one example, targeting individuals  who possess “unique operational skills.”

Read more reporting by Michael Isikoff in 'The Isikoff Files'

Brennan  said the use of drones gives U.S. intelligence agencies the ability to use “laser-like” precision against the terrorists. But he acknowledged that "innocent civilians have been killed in these strikes." He said such instances have been "exceedingly rare, but it has happened.

“When it does, it pains us and we regret it deeply, as we do any time innocents are killed in war," he added. 

That passage of his speech alone was significant. In June 2011, Brennan said that in the previous year of operations in the government’s then-unspecified program to eliminate al-Qaida members, “There hasn’t been a single collateral death because of the exceptional proficiency, precision of the capabilities we’ve been able to develop.”   

Brennan later changed that statement in response to questions by the New York Times, spurred in part by  reports about a May 6 strike in Pakistan that  hit a religious school, an adjourning restaurant and a house, killing 18 people. Although 12 militants were allegedly killed, British and Pakistani journalists on the scene reported that six civilians also died in the strike.

In Brennan’s adjusted statement last year, he said, “Fortunately, for more than a year, due to our discretion and precision, the U.S. government has not found credible evidence of collateral deaths resulting from U.S. counterterrorism operations outside of Afghanistan or Iraq.”

Brennan did not give any details on Monday about how rare civilian deaths have been. But according to the analysis by the New America Foundation, which relies heavily on local media and other reports from observers in Pakistan, about 17 percent of those who have been killed by drones since the program effectively began in 2004 were “non-militants.”  The foundation estimated that the  “non-military fatality rate” has since dropped to about 13 percent under Obama – as drone strikes have become more frequent and more precise.

Those numbers translate to 471 civilian deaths, including 309 under Obama.

Human rights groups — who have challenged the administration to be more open about its drone program — were not satisfied with the new details provided by Brennan’s speech.

“It is not enough that care is taken to avoid harm to innocent civilians,” said Raha Wala, an official with Human Rights First. “Brennan's assertion that any 'member' of al-Qaida or 'associated forces' is legally targetable is wrong. Under the laws of armed conflict, only members of the enemy's armed forces, or those directly participating in hostilities or who perform a continuous combat function, may be targeted.”

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The war against al-Qaida is at a “critical moment” as the “much weaker” terrorist group looks to regroup in Africa, according to the author of a new report.

Valentina Soria, a counterterrorism research analyst at U.K. think-tank RUSI, told msnbc.com by telephone that the network had been damaged by the death of Osama bin Laden and other leading figures.

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Her report, titled “Global Jihad Sustained Through Africa,” which was published at 7 p.m. ET Tuesday, said al-Qaida’s leadership was looking for partnerships with like-minded organizations in parts of Africa – such as al-Shabab and al-Qaida in the Islamic Maghreb -- to “regroup and re-energize itself.”

West 'unsighted' by shift
Soria told msnbc.com that the war on terror was at a key point, as while al-Qaida was weaker, Western counterterrorism officials had been “unsighted” by the apparent shift to Africa.

“I think it’s certainly an important junction, a critical moment because obviously counterterrorism operations in Afghanistan and Pakistan … and Yemen have been quite successful in decapitating the organization [al-Qaida], a lot of important figures have been removed,” Soria said.

“There is no doubt the organization is much weaker than it was a few years ago,” she added.

The report said that “despite greater co-operation, there seems to be an unresolved tension between transnational aims of al-Qaida-core and the local grievances of African partners.”

It added it was unclear whether al-Qaida was making a “conscious effort” to regroup in the Horn of Africa and sub-Saharan Africa or if this was the result of “displacement” and cooperation on an “ad hoc basis.”

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Islamist militant group al-Shabab, which operates in Somalia, has merged with al-Qaida’s core group, a move “officially endorsed” by al-Qaida’s leader Ayman al-Zawahiri in February of this year.

'Arc of regional instability'
The report noted that U.S. counterterrorism officials had been voicing concern about the prospect of al-Qaida in the Islamic Maghreb, which is based in Algeria, using local instability and weak or absent government to expand its zone of influence.

“If correct, this assessment would raise the worrying prospect of an arc of regional instability encompassing the whole Sahara-Sahel strip and extending to east Africa, which the now weakened al-Qaida-core could well exploit to regroup, reorganize and reinvigorate its terrorist campaign in the West,” the report said.

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 “[Al-Qaida] appears to be adopting a strategy of ‘going native,’ which implies seizing upon and exploiting local grievances with the ultimate aim of securing a stable foothold in volatile countries,” the report said.

The report said that counterterrorism officials “privately acknowledge that they are unsighted” and are “working hard to understand how far the jihadist challenge may be migrating” to Somalia, Kenya, north Nigeria and parts of West Africa.

“From West to East Africa, across the Sub-Saharan region, we may well be witnessing a new phase of decisive developments that could trigger further turmoil,” the report said.

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