With Brennan's team now in the lead, consulting with the State Department and other agencies as to who should go on the list, a previous military-run review process in place since 2009 has become less relevant, according to two current and three former U.S. officials aware of the evolution in how the government targets terrorists.
In describing Brennan's arrangement to The Associated Press, the officials provided the first detailed description of the military's previous review process that set a schedule for killing or capturing terror leaders around the Arab world and beyond. They spoke on condition of anonymity because U.S. officials are not allowed to publicly describe the classified targeting program.
One senior administration official argues that Brennan's move adds another layer of review that augments rather than detracts from the Pentagon's role. The Pentagon can still carry out its own internal procedures to make recommendations to the secretary of defense, the official said.
But Brennan would still be the one to approve the final recommendation to President Barack Obama. And officials outside the White House expressed concern that drawing more of the decision-making process to Brennan's office could turn it into a pseudo military headquarters, entrusting the fate of al-Qaida targets to a small number of senior officials.
Under the new plan, Brennan's staff compiles the potential target list and runs the names past agencies such as the State Department at a weekly White House meeting, the officials said.
Previously, targets were first discussed in meetings run by the chairman of the Joint Chiefs of Staff, Adm. Mike Mullen at the time, with Brennan being just one of the voices in the debate. Brennan ultimately would make the case to the president, but a larger number of officials would end up drawn into the discussion.
The new Joint Chiefs chairman, Gen. Martin Dempsey, has been more focused on shrinking the U.S. military as the Afghan war winds down and less on the covert wars overseas.
With Dempsey less involved, there is an even greater need to draw together different agencies' viewpoints, some in the administration believe, showing the American public that al-Qaida targets are chosen only after painstaking and exhaustive debate. This could be especially true in an election year, when drone strikes can be politically sensitive.
Some of the officials carrying out the policy are equally leery of "how easy it has become to kill someone," one said. The U.S. is targeting al-Qaida operatives for reasons such as being heard in an intercepted conversation plotting to attack a U.S. ambassador overseas, the official said. Stateside, that conversation could trigger an investigation by the Secret Service or FBI.
The CIA and the Pentagon did not respond to requests for comment.
Drone strikes are highly controversial in Pakistan, too. Obama met briefly on the sidelines of the NATO summit in Chicago on Monday with Pakistani President Asif Ali Zardari and Afghan President Hamid Karzai.
Pakistan has closed key transit routes used by NATO to send supplies to troops in Afghanistan in response to a U.S. airstrike that killed two dozen Pakistani soldiers.
An example of a recent Pentagon-led drone strike was the fatal attack in January on al-Qaida commander Bilal al-Berjawi in Somalia. U.S. intelligence and military forces had been watching him for days. When his car reached the outskirts of Mogadishu, the drones fired a volley of missiles, obliterating his vehicle and killing him instantly. The drones belonged to the elite U.S. Joint Special Operations Command. The British-Lebanese citizen al-Berjawi ended up on the JSOC list after a studied debate run by the Pentagon.
The Defense Department's list of potential drone or raid targets is about two dozen names long, the officials said. The previous process for vetting them, now mostly defunct, was established by Mullen early in the Obama administration, with a major revamp in the spring of 2011, two officials said.
Drone attacks were split between JSOC and the CIA, which keeps a separate list of targets, though it overlaps with the Pentagon list. By law, the CIA can target only al-Qaida operatives or affiliates who directly threaten the U.S. JSOC has a little more leeway, allowed by statue to target members of the larger al-Qaida network.
Under the old Pentagon-run review, the first step was to gather evidence on a potential target. That person's case would be discussed over an interagency secure video teleconference, involving the National Counterterrorism Center and the State Department, among other agencies. Among the data taken into consideration: Is the target a member of al-Qaida or its affiliates; is he engaged in activities aimed at the U.S. overseas or at home?
If a target isn't captured or killed within 30 days after he is chosen, his case must be reviewed to see if he's still a threat.
The CIA's process is more insular. Only a select number of high-ranking staff can preside over the debates run by the agency's Covert Action Review Group, which then passes the list to the CIA's Counterterrorism Center to carry out the drone strikes. The Director of National Intelligence, Jim Clapper, is briefed on those actions, one official said.
Al-Berjawi's name was technically on both lists - the Pentagon's, and the CIA's. In areas where both JSOC and the CIA operate, the military task force commander and CIA chief of station confer, together with representatives of U.S. law enforcement, on how best to hit the target. If it's deemed possible to grab the target, for interrogation or simply to gather DNA to prove the identity of a deceased person, a special operations team is sent, as in the case of the 2009 Navy SEAL raid against al-Qaida commander Saleh Ali Saleh Nabhan. Nabhan's convoy was attacked by helicopter gunships, after which the raiders landed and took his body for identification, before burying him at sea.
But if the al-Qaida operative is in transit from Somalia to Yemen by boat, for instance, U.S. security officials might opt to use the Navy to intercept and the FBI to arrest him, officials said.
Human rights and civil liberties groups have argued for the White House to make public the legal process by which names end up on the targeting lists.
"We continue to believe, based on the information available, that the (drone) program itself is not just unlawful but dangerous," said Hina Shamsi, director of the ACLU National Security Project. "It is dangerous to characterize the entire planet as a battlefield."
Shrinking the pool of people deciding who goes on the capture/kill list means fewer people to hold accountable, said Mieke Eoyang from Third Way, a centrist Democratic think tank.
"As a general principle, if people think someone is checking their work, they are more careful," Eoyang said. "Small groups can fall victim to group-think."
Brennan gave a landmark speech last month describing the Obama administration's legal reasoning behind the drone program. He said the choice of targets is weighed by whether capture is possible vs. the level of threat the person presents to Americans. He argued such targets are not civilians, but akin to targeting Japanese or German commanders in World War II.