If history is any judge, President Bush may soon regret he chose a military man to run the nation’s civilian spy service, the CIA.

Three of the flag-rank military officers presidents chose to run the CIA since 1947 have struggled in the job, the record shows, with one of them fired in less than a year.

But since history is often wrong as a guide — and an Army officer was one of the CIA’s best leaders a half century ago — Bush’s choice of Air Force General Michael V. Hayden may be just what he needs for his final two years in office.

There’s no doubt the four-star general, Bush’s choice to be the CIA’s 18th leader in its almost 60-year history (not counting temporary directors), will face contentious confirmation hearings over the secret, warrant-less wiretaps carried out while Hayden was running the eavesdropping National Security Agency.

Hayden will also likely be asked whether he has any ties to military contractors at the center of a corruption scandal ignited by the confession of former Rep. Randy “Duke” Cunningham, R-Calif., that he took bribes to help a private company get contracts for intelligence work.

Lastly but hardly least, the nominee is also likely to face probing questions about the “militarization” of the spy agency if he got the job, especially with Republican Sen. Susan Collins of Maine, chairwoman of the Government Operations and Homeland Security Committee, suggesting Hayden should hang up his uniform before he takes the CIA job. But with at least one key Senate Intelligence Committee Democrat, Dianne Feinstein of California, in his corner, Hayden’s rough voyage to confirmation is likely to succeed.

Unless something unexpected turns up — always a possibility in such a charged political environment — Hayden’s hearings are not likely to run aground like President John F. Kennedy’s pick for CIA.

In late 1961, Kennedy had nominated industrialist John McCone to be the nation’s top spy following the disastrous, agency-led 1961 invasion of Cuba. McCone nomination drew 11 negative votes in the Armed Services Committee, which then held oversight for the CIA, forcing Kennedy to make a recess appointment. McCone was later confirmed.

McCone quit in 1965 when President Lyndon B. Johnson began accepting the Pentagon’s optimistic forecasts for victory in Vietnam, which were considerably more rosy than the CIA’s.

The CIA had been created in 1947 precisely to balance such hawkish analysis by the Pentagon. President Truman and other civilian leaders were convinced that the Pentagon’s estimates of foreign threats were tainted by a thirst for more and bigger weapons. They wanted a new, independent center of analysis, as well as a cadre of spies to steal secrets, to counterbalance the Pentagon.

Sending a military man out to run the CIA blurs the dividing line, the critics of Hayden’s nomination say.

But the CIA is a far different place than before the directorate of national intelligence was created to ride herd over it and the other 15 U.S. spy agencies. Now it’s just another secret intelligence service, albeit one with a special mission and talents.

“The historic fear about military leaders heading the CIA is that they will make it a more pro-military agency, more pro-war, more likely to serve military interests,” says David Barrett, author of “The CIA and Congress: The Untold Story From Truman to Kennedy,” “and that the agency will not be independent in writing its analyses and estimates.”

With one exception, Barrett says, “The track record of military leaders as [CIA] director is not very good, though my view is that their more-or-less failed performances were not specifically because of their military leadership history or background.”

“None of them felt especially at home in the job,” Barrett said. “None was a shrewd political actor in the . . . job.

The exception was Gen. Walter Bedell Smith, CIA director from 1950 to 1953, under Truman, Barrett says.

“Tough, smart, determined, goal-oriented, practical sense,” Barrett said via e-mail. “He told the president and congressional leaders and others exactly what the CIA thought and what he thought. He reformed our covert action efforts and eliminated waste.”

Barrett’s nominations for “failures”:

• Adm. Roscoe Hillenkoetter, 1947-1950, under Truman.

“The CIA’s first director could not navigate the shark-infested waters of Washington, with many agencies hating the new CIA. There was much failed covert action, too. However, he privately stood up to [Wisconsin] Sen. Joe McCarthy on alleged communists and gays in the CIA.”

• Adm. William Raborn, 1965-66, under President Johnson.

“Incompetent at CIA, not understanding the agency or the intelligence business. Eased out by LBJ, who realized he had made a mistake, after a year.”

• Adm. Stansfield Turner, 1977-81, under President Carter.

“He fired large numbers of CIA officers abruptly and coldly and created a hostile environment there for the next four years. He did oversee somewhat successful covert action in Afghanistan against the Soviets, though.”

Peter Brookes, a former CIA officer and Defense Department official, said “a lot of people are concerned” that Hayden “could have a tenure like Stansfield Turner,” which he called ”very, very bad . . . a dark period” at the CIA, especially for its operations directorate, where the agency’s spying and covert actions are carried out.

But like others who predict that that Hayden will turn out to be a dynamic defender of CIA turf and counterweight to Defense Secretary Donald H. Rumsfeld’s aggressive expansion of military intelligence activities, Brookes said such concerns are unfounded.

“The important thing, Brookes said, “is to find somebody who has run a large intelligence organization, and Bush has.”

Jeff Stein can be reached at jstein@cq.com.