By Phil Stewart and Mark Hosenball

WASHINGTON (Reuters) – Newly retired General David Petraeus is well aware that his swearing-in as the next director of the CIA, expected on Tuesday, might stoke concerns about the “militarization” of the U.S. spy agency.

It was one of the reasons the storied battlefield commander hung up his uniform last week after a 37-year career in the Army. It may also be why he appears so intent on fulfilling a pledge to leave his military entourage — “braintrusts” as he calls them — behind when he arrives at the CIA’s Langley, Virginia, compound.

But even as he surrounds himself with civilian advisors, a process sources say is well under way, questions remain about the influence Petraeus might have on the CIA, both analytically and in its use of lethal force against al Qaeda.

Petraeus cannot be expected to divorce himself from a view shared at the highest levels of the U.S. military that the Afghan war is broadly trending in the right direction and that the Taliban’s momentum has been reversed. The CIA has been more cautious in its assessment of the decade-old conflict than the military.

How Petraeus will reconcile those visions of the war effort he commanded until July, and reassure CIA analysts of his objectivity, could be one of the biggest challenges facing the Army general in this transition.

Then there are larger questions about the blurred lines between covert CIA operations and military ones in the battle against al Qaeda — including the CIA’s armed Predator drone campaign in Pakistan, a program which appears to have scored a major victory with an August 22 strike that killed al Qaeda’s No. 2.

Petraeus attempted to address the issue head-on at his confirmation hearing in June, saying one of the reasons he was retiring from the military — even though no law compelled him to do so — was to allay concerns about the militarization of the CIA. He also said he would seek to represent the “Agency position” on matters including the war in Afghanistan.

“Beyond that, I have no plans to bring my military brain trust with me to the agency,” Petraeus said at the time.

“There is no shortage of impressive individuals at the agency, and I look forward to interacting with them and populating my office with them.”

“If confirmed, I will, in short, get out of my vehicle alone on the day that I report to Langley.”

NONMILITARY CHIEF OF STAFF

To that end, sources tell Reuters that a longtime CIA insider — not one of Petraeus’ “guys” — has been named as his new chief of staff. One person familiar with the matter identified him as Rodney Snyder, who has previously worked on the White House national security staff. But U.S. officials would not immediately confirm that name.

A U.S. official close to the general said Petraeus remarked recently to a friend that he believed every member of the existing CIA leadership team was a “strong swimmer.”

“There are always a few vacancies when one director leaves, and General Petraeus is working with the rest of the agency’s leadership team to fill those,” the official said.

One example is the post of CIA director of congressional affairs. When the last CIA director, Leon Panetta, left the agency to become defense secretary in July, the person who held that post also went to the Pentagon to fill a top job.

Petraeus’ supporters say the veteran military leader, known for his political savvy and sharp intellect — he holds a doctoral degree from Princeton — is more than capable of succeeding as CIA director.

Still, the obstacles facing him are daunting. The CIA recently completed an updated “District Assessment on Afghanistan,” which remains classified.

Washington Post columnist David Ignatius, citing one military official, said the document used the word “stalemate” to describe the conflict and did not adhere to U.S. military claims that the Taliban’s momentum had been reversed.

Petraeus, in his Army retirement speech on August 31, cited “progress against al Qaeda and the reversal of Taliban momentum in Afghanistan.”

That is not Petraeus’ only challenge. He is expected as CIA director to embrace the campaign of drone strikes in Pakistan, a nominally covert CIA operation that has fueled anti-American sentiment but put heavy pressure on militant safe havens.

But continuing or stepping up drone attacks risks further straining relations between the CIA and Pakistan’s Inter-Services Intelligence directorate.

(Additional reporting by Toby Zakaria; Editing by Todd Eastham)