If Brennan's Confirmed, Spy Staffers May Ask 'Who's the Boss?'

(CNN) -- Creating the office of the director of national intelligence in 2005 was meant to improve the management of the nation's intelligence gathering in the wake of 9/11, but it has often led to turf wars between national intelligence directors and directors of the CIA.

Now President Barack Obama's nomination of his trusted counterterrorism aide, John Brennan, as CIA director may leave the impression that the CIA director is the top spy, even though the director of national intelligence technically would be his boss.

The problem, past directors in both posts and other experts say, is that the DNI's role is ambiguous.

The job of DNI was created to reform the intelligence community after the September 11, 2001, terrorist attacks and the faulty intelligence that suggested Iraq had weapons of mass destruction.

Before that time, the CIA director not only ran the spy agency but also had a second title, director of central intelligence, which was responsible for coordinating the activities of the 16 agencies and departments that make up the intelligence community.

An independent commission that reviewed the intelligence failures concluded, and Congress agreed, that one person should focus exclusively on guiding the community. Running the CIA, the review concluded, was a full-time job on its own.

Thus began the role of the director of national intelligence, who runs the entire community and is the chief intelligence adviser to the president. It was not long before tension emerged.

In 2009, outgoing CIA Director Michael Hayden told reporters that there is a natural tension between the CIA and DNI, but "it's not a bad structure."

However, he did suggest that the DNI's office was getting a bit bloated and said, "Americans being Americans, they're going to fill up their day trying to do something impactful, which means between the two of us, there's going to be a trench line."

Also departing at the same time was national intelligence director Mike McConnell. His response to Hayden's observation: "Any time you have organizations with similar interests, you're going to have disputes, and particularly if the two leaders aren't working together and having a partnership ... the warfare at the trench level gets to be pretty much a raging battle," he said. "We don't have a department of intelligence. If this were the Department of Defense, there wouldn't be any question, but it isn't."

Soon afterward, their successors, DNI Dennis Blair and CIA Director Leon Panetta, butted heads.

Because he led the intelligence community, Blair wanted control over who would be the chief spy in any given country, not necessarily relying on the CIA's station chief. He also wanted more say in covert operations. Panetta wasted no time letting the White House know he was not prepared to lose authority over either.

James Jones, then the national security adviser, mediated the dispute and ultimately decided the CIA would have a direct line to the West Wing on covert operations and retain control over choosing the top spy in each country.

It was the beginning of the end for Blair, who was later forced out.

Lee Hamilton, who was co-chairman of the 9/11 Commission, has often said the intelligence reform legislation was too "ambiguous," and as long as it remains that way, the DNI and CIA director will fight for jurisdiction and power.

Add to that burning fire the fuel of Brennan. If he gets the CIA job, a person who just spent the past four years in the White House as the President's most trusted aide on counter terrorism and intelligence matters will lead the agency. Now Brennan can walk into the Oval Office or directly call Obama any time of the day or night when there is a crisis. Often in Washington, the ultimate sign of power is one's proximity to the president.

Brennan will lose some of that when he moves across the river to Langley.

He will still report directly to Obama on covert operations, but otherwise his boss will be DNI James Clapper, ostensibly the president's principle intelligence adviser. But for the last four years, Washington insiders came to believe that Brennan was, for all intents and purposes, filling that role while in the West Wing.

"Brennan has sort of become the de facto senior intelligence adviser to the president," said Frances Fragos Townsend, who held a similar position to Brennan's at the White House during the Bush administration.

A former senior intelligence official who would only speak on the condition of anonymity said within the Obama administration, there is a different metric.

"Checking the plumbing and keeping the trains running on time really is what the DNI is doing, and the president is looking elsewhere for that final, critical, definitive intelligence advice," the official said.

Will that advice come predominantly from Brennan, who has had such open access to the president, rather than Clapper, effectively bypassing him?

Jones, who has worked firsthand with both Brennan and Clapper, doesn't foresee any real turf battles, even though the two men will not always agree.

"John Brennan and Gen. Clapper are two of the most consummate professionals I have ever worked with," said Jones, a former national security adviser to Obama. He believes "they will work hand-in-glove together."

The two men do have a history of working together in the intelligence community, especially over the past four years.

"Every indication I've ever had is that they like and respect each other," Townsend said, adding she was unaware of any major disagreement between them.

When asked by CNN if Clapper believed his authority as head of the intelligence community would be in any way compromised by Brennan being CIA chief, DNI spokesman Shawn Turner said: "Director Clapper leads the intelligence community, and he's always had great relationships with the directors of the (other) agencies, especially the CIA. That will not change when John is at the helm at the agency. He and the DNI are longtime friends and colleagues. They have always trusted and respected each other in their respective roles and I'm confident that will continue to be the case."

And the bottom-line, according to Townsend, is not whether the national intelligence director or CIA director is considered the president's senior intelligence adviser; every president will have his own model.

It's about getting the job done, and providing the president with accurate, timely and effective advice.

"If you make it about the mission and where the capability lies, and these two guys put their egos aside, then you ought to be OK," Townsend said.

And Jones said that's what these two will do. "It's not about them. These are two people whose egos are completely in check."

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