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SANA, Yemen — Late last August, a 40-year-old cleric named Salem Ahmed bin Ali Jaber stood up to deliver a speech denouncing Al Qaeda in a village mosque in far eastern Yemen.

John Brennan

Members of the Kaual tribe in the capital, Sana, on Tuesday.  Two of their relatives died in a drone strike last month, they said.

"He's probably had more power and influence than anyone in a comparable position on the last 20 years." David Benjamin, a former top counterterrorism official at the State Department, speaking about John O. Brennan, President Obama's choice to lead the C.I.A.

It was a brave gesture by a father of seven who commanded great respect in the community, and it did not go unnoticed. Two days later, three members of Al Qaeda came to the mosque in the tiny village of Khashamir after 9 p.m., saying they merely wanted to talk. Mr. Jaber agreed to meet them, bringing his cousin Waleed Abdullah, a police officer, for protection.

As the five men stood arguing by a cluster of palm trees, a volley of remotely operated American missiles shot down from the night sky and incinerated them all, along with a camel that was tied up nearby.

The killing of Mr. Jaber, just the kind of leader most crucial to American efforts to eradicate Al Qaeda, was a reminder of the inherent hazards of the quasi-secret campaign of targeted killings that the United States is waging against suspected militants not just in Yemen but also in Pakistan and Somalia. Individual strikes by the Predator and Reaper drones are almost never discussed publicly by Obama administration officials. But the clandestine war will receive a rare moment of public scrutiny on Thursday, when its chief architect, John O. Brennan, the White House counterterrorism adviser, faces a Senate confirmation hearing as President Obama's nominee for C.I.A. director.

From his basement office in the White House, Mr. Brennan has served as the principal coordinator of a "kill list" of Qaeda operatives marked for death, overseeing drone strikes by the military and the C.I.A., and advising Mr. Obama on which strikes he should approve.

"He's probably had more power and influence than anyone in a comparable position in the last 20 years," said Daniel Benjamin, who recently stepped down as the State Department's top counterterrorism official and now teaches at Dartmouth. "He's had enormous sway over the intelligence community. He's had a profound impact on how the military does counterterrorism."

Mr. Brennan, a former C.I.A. station chief in Riyadh, Saudi Arabia, has taken a particular interest in Yemen, sounding early alarms within the administration about the threat developing there, working closely with neighboring Saudi Arabia to gain approval for a secret C.I.A. drone base there that is used for American strikes, and making the impoverished desert nation a test case for American counterterrorism strategy.

In recent years, both C.I.A. and Pentagon counterterrorism officials have pressed for greater freedom to attack suspected militants, and colleagues say Mr. Brennan has often been a restraining voice. The strikes have killed a number of operatives of Al Qaeda in the Arabian Peninsula, the terrorist network's affiliate in Yemen, including Said Ali al-Shihri, a deputy leader of the group, and the American-born cleric Anwar al-Awlaki.

But they have also claimed civilians like Mr. Jaber and have raised troubling questions that apply to Pakistan and Somalia as well: Could the targeted killing campaign be creating more militants in Yemen than it is killing? And is it in America's long-term interest to be waging war against a self-renewing insurgency inside a country about which Washington has at best a hazy understanding?

Several former top military and intelligence officials — including Stanley A. McChrystal, the retired general who led the Joint Special Operations Command, which has responsibility for the military's drone strikes, and Michael V. Hayden, the former C.I.A. director — have raised concerns that the drone wars in Pakistan and Yemen are increasingly targeting low-level militants who do not pose a direct threat to the United States.

In an interview with Reuters, General McChrystal said that drones could be a useful tool but were "hated on a visceral level" in some of the places where they were used and contributed to a "perception of American arrogance."

Mr. Brennan has aggressively defended the accuracy of the drone strikes, and the rate of civilian casualties has gone down considerably since the attacks began in Yemen in 2009. He has also largely dismissed criticism that the drone campaign has tarnished America's image in Yemen and has been an effective recruiting tool for Al Qaeda.

"In fact, we see the opposite," Mr. Brennan said during a speech last year. "Our Yemeni partners are more eager to work with us. Yemeni citizens who have been freed from the hellish grip of A.Q.A.P. are more eager, not less, to work with the Yemeni government."

Christopher Swift, a researcher at Georgetown University who spent last summer in Yemen studying the reaction to the strikes, said he thought Mr. Brennan's comments missed the broader impact.

"What Brennan said accurately reflected people in the security apparatus who he speaks to when he goes to Yemen," Mr. Swift said. "It doesn't reflect the views of the man in the street, of young human rights activists, of the political opposition."

Though Mr. Swift said he thought that critics had exaggerated the role of the strikes in generating recruits for Al Qaeda, "in the political sphere, the perception is that the U.S. is colluding with the Yemeni government in a covert war against the Yemeni people."

"Even if we're winning in the military domain," Mr. Swift said, "drones may be undermining our long-term interest in the goal of a stable Yemen with a functional political system and economy."

A Parallel Campaign

American officials have never explained in public why the C.I.A. and the Pentagon's Joint Special Operations Command are carrying out parallel drone campaigns in Yemen. Privately, however, they describe an arrangement that has evolved since the frantic, ad hoc early days of America's war there.

The first strike in Yemen ordered by the Obama administration, in December 2009, was by all accounts a disaster. American cruise missiles carrying cluster munitions killed dozens of civilians, including many women and children. Another strike, six months later, killed a popular deputy governor, inciting angry demonstrations and an attack that shut down a critical oil pipeline.

Not long afterward, the C.I.A. began quietly building a drone base in Saudi Arabia to carry out strikes in Yemen. American officials said that the first time the C.I.A. used the Saudi base was to kill Mr. Awlaki in September 2011.

Since then, officials said, the C.I.A. has been given the mission of hunting and killing "high-value targets" in Yemen — the leaders of Al Qaeda in the Arabian Peninsula who Obama administration lawyers have determined pose a direct threat to the United States. When the C.I.A. obtains specific intelligence on the whereabouts of someone on its kill list, an American drone can carry out a strike without the permission of Yemen's government.

There is, however, a tighter leash on the Pentagon's drones. According to American officials, the Joint Special Operations Command must get the Yemeni government's approval before launching a drone strike. This restriction is in place, officials said, because the military's drone campaign is closely tied to counterterrorism operations conducted by Yemeni special operations troops.

Yemen's military is fighting its own counterinsurgency battle against Islamic militants, who gained and then lost control over large swaths of the country last year. Often, American military strikes in Yemen are masked as Yemeni government operations.

Moreover, Mr. Obama demanded early on that each American military strike in Yemen be approved by a committee in Washington representing the national security agencies. The C.I.A. strikes, by contrast, resulted from a far more closed process inside the agency. Mr. Brennan plays a role in overseeing all the strikes.

There have been at least five drone strikes in Yemen since the start of the year, killing at least 24 people. That continues a remarkable acceleration over the past two years in a program that has carried out at least 63 airstrikes since 2009, according to The Long War Journal, a Web site that collects public data on the strikes, with an estimated death toll in the hundreds. Many of the militants reported killed recently were very young and do not appear to have had any important role with Al Qaeda.

"Even with Al Qaeda, there are degrees — some of these young guys getting killed have just been recruited and barely known what terrorism means," said Naji al Zaydi, a former governor of Marib Province, who has been a vocal opponent of Al Qaeda and a supporter of Yemen's president, Abdu Rabbu Mansour Hadi.

Mr. Zaydi, a prominent tribal figure from an area that has long been associated with members of Al Qaeda's Yemeni affiliate, pointed out that the identity and background of these men were no mystery in Yemen's interlinked tribal culture.

A Deadly Ride

In one recent case, on Jan. 23, a drone strike in a village east of Sana killed a 21-year-old university student named Saleem Hussein Jamal and his cousin, a 33-year-old teacher named Ali Ali Nasser Jamal, who happened to have been traveling with him. According to relatives and neighbors of the two men, they were driving home from a nearby town called Jahana when five strangers offered to pay them for a ride. The drone-fired missile hit the vehicle, a twin-cab Toyota Hilux, just outside the village of Masnaa at about 9 p.m. The strangers were later identified in Yemeni news reports as members of Al Qaeda, though apparently not high-ranking ones.

After the strike, villagers were left to identify their two dead relatives from identity cards, scraps of clothing and the license plate of Mr. Jamal's Toyota; the seven bodies were shredded beyond recognition, as cellphone photos taken at the scene attest. "We found eyes, but there were no faces left," said Abdullah Faqih, a student who knew both of the dead cousins.

Although most Yemenis are reluctant to admit it publicly, there does appear to be widespread support for the American drone strikes that hit substantial Qaeda figures like Mr. Shihri, a Saudi and the affiliate's deputy leader, who died in January of wounds received in a drone strike late last year.

Al Qaeda has done far more damage in Yemen than it has in the United States, and one episode reinforced public disgust last May, when a suicide bomber struck a military parade rehearsal in the Yemeni capital, killing more than 100 people.

Moreover, many Yemenis reluctantly admit that there is a need for foreign help: Yemen's own efforts to strike at the terrorist group have often been compromised by weak, divided military forces; widespread corruption; and even support for Al Qaeda within pockets of the intelligence and security agencies.

Yet even as both Mr. Brennan and Mr. Hadi, the Yemeni president, praise the drone technology for its accuracy, other Yemenis often point out that it can be very difficult to isolate members of Al Qaeda, thanks to the group's complex ties and long history in Yemen.

This may account for a pattern in many of the drone strikes: a drone hovers over an area for weeks on end before a strike takes place, presumably waiting until identities are confirmed and the targets can be struck without anyone else present.

In the strike that killed Mr. Jaber, the cleric, that was not enough. At least one drone had been overhead every day for about a month, provoking high anxiety among local people, said Aref bin Ali Jaber, a tradesman who is related to the cleric. "After the drone hit, everyone was so frightened it would come back," Mr. Jaber said. "Children especially were affected; my 15-year-old daughter refuses to be alone and has had to sleep with me and my wife after that."  

Anger at America

In the days afterward, the people of the village vented their fury at the Americans with protests and briefly blocked a road. It is difficult to know what the long-term effects of the deaths will be, though some in the town — as in other areas where drones have killed civilians — say there was an upwelling of support for Al Qaeda, because such a move is seen as the only way to retaliate against the United States.

Innocents aside, even members of Al Qaeda invariably belong to a tribe, and when they are killed in drone strikes, their relatives — whatever their feelings about Al Qaeda — often swear to exact revenge on America.

"Al Qaeda always gives money to the family," said Hussein Ahmed Othman al Arwali, a tribal sheik from an area south of the capital called Mudhia, where Qaeda militants fought pitched battles with Yemeni soldiers last year. "Al Qaeda's leaders may be killed by drones, but the group still has its money, and people are still joining. For young men who are poor, the incentives are very strong: they offer you marriage, or money, and the ideological part works for some people."

In some cases, drones have killed members of Al Qaeda when it seemed that they might easily have been arrested or captured, according to a number of Yemeni officials and tribal figures. One figure in particular has stood out: Adnan al Qadhi, who was killed, apparently in a drone strike, in early November in a town near the capital.

Mr. Qadhi was an avowed supporter of Al Qaeda, but he also had recently served as a mediator for the Yemeni government with other jihadists, and was drawing a government salary at the time of his death. He was not in hiding, and his house is within sight of large houses owned by a former president of Yemen, Ali Abdullah Saleh, and other leading figures.  

Whatever the success of the drone strikes, some Yemenis wonder why there is not more reliance on their country's elite counterterrorism unit, which was trained in the United States as part of the close cooperation between the two countries that Mr. Brennan has engineered. One member of the unit, speaking on the condition of anonymity, expressed great frustration that his unit had not been deployed on such missions, and had in fact been posted to traffic duty in the capital in recent weeks, even as the drone strikes intensified.

"For sure, we could be going after some of these guys," the officer said. "That's what we're trained to do, and the Americans trained us. It doesn't make sense."

Robert F. Worth reported from Sana, and Mark Mazzetti and Scott Shane from Washington.