Gates Confirmed as CIA Director : Intelligence: The Senate’s 64-31 vote ends the longest confirmation process in the agency’s history. But doubts linger among many Democratic lawmakers.

The Senate, concluding the longest and most controversial confirmation process ever undertaken for a director of central intelligence, voted Tuesday to approve the nomination of Robert M. Gates to head the CIA.

Embracing the argument that the scandal-plagued agency needs an experienced insider to help redefine its mission in the wake of the Cold War, 22 Democrats joined with 42 Republicans to confirm Gates by a vote of 64 to 31.

President Bush--who had fought vigorously to ensure Gates’ confirmation in spite of doubts about how much the nominee knew about the Iran-Contra scandal and allegations that he had changed intelligence estimates in the 1980s for political reasons--said the vote affirmed that “Bob Gates has the professional expertise and experience to lead our intelligence community during these changing times.”

A 20-year CIA veteran, Gates, 48, has served as Bush’s deputy national security adviser for the last three years. He becomes the first career intelligence officer to head the agency since William E. Colby served as director in the mid-1970s.

In a written statement, Bush, who served as director of central intelligence during the 1970s, said that he looks forward to Gates “undertaking his duties quickly . . . (and) guiding our intelligence community during this historic era.”

For Gates, the margin of victory represented a personal triumph over the suspicions that have stalked his career since 1987, when he was first chosen to head the CIA. He was forced to withdraw then because of questions about his possible role in the Iran-Contra scandal during the years he served as deputy to the late CIA Director William J. Casey.

While critics maintained that many of those questions are still unanswered, it was clear from the vote that Democrats remained deeply divided over attempts to resurrect the Iran-Contra scandal as a political issue. It was also clear from the outcome that many Democrats were not eager to engage in another bruising confirmation battle so soon after the controversy over Clarence Thomas’ appointment to the Supreme Court.

Several senators admitted privately that memories of the Thomas debacle were a major factor in their decision to vote for the nominee. New Jersey Democrat Bill Bradley, who led the opposition to Gates, said that some Democratic senators had told him openly that, “because they had gone against Thomas, they were going to vote for Gates.”

Some senators said that three factors proved pivotal in swinging the vote solidly in favor of Gates: Bush’s insistence on having him at the CIA, the strong track record that Gates himself established in recent years in keeping Congress informed of intelligence activities and the absence--despite weeks of hearings and hundreds of depositions--of conclusive proof that he knew more about the Iran-Contra scandal than he has admitted.

Nevertheless, although many Democrats said that they found no “smoking gun” to disqualify the nominee, they said that they were voting for Gates only with strong reservations about his suitability for the job.

Indeed, the highly qualified--in some instances, even antagonistic--endorsements of key Democrats such as Sens. Sam Nunn of Georgia and Patrick J. Leahy of Vermont made it clear that Gates will return to the CIA under a different cloud--one that stems from new allegations that he slanted intelligence assessments to suit the biases and further the policy objectives of Casey and other senior officials in the Ronald Reagan Administration.

“It was a close call,” said Nunn, who indicated that he was voting for Gates even though he did not think he was the best choice for the job. “I still have reservations because of allegations of politicization. . . . I have questions about whether he’s the right man for the job.” Nunn added that he was voting for Gates only reluctantly because “I don’t find anything to disqualify him at this point.”

Leahy, a former vice chairman of the Intelligence Committee who now chairs the Appropriations subcommittee that controls foreign aid, summed up the ambivalence that most Democrats who voted in favor of Gates expressed either publicly or privately before the vote.

Gates “carries a heavy load on his shoulders. . . . Fairly or not, he bears the legacy of the Casey years, when deceit, misinformation, illegal operations and . . . misleading of the oversight committees and Congress were the norm,” Leahy said.

Yet with “all his flaws and with all the clouds hanging over him,” the evidence of wrongdoing on Gates’ part is inconclusive and he remains “far more qualified than . . . anyone the White House is likely to put forward if he is not confirmed,” Leahy added.

Gates’ more ardent supporters also took that line, arguing that America’s next spymaster must be someone of experience. They cited the major changes that will have to be made at the CIA to retarget its resources in a world in which the Soviet Union is no longer a major military threat and in which budget constraints are likely to result in steep cutbacks in the CIA’s estimated $30-billion-a-year budget.

“The last thing you want is someone at the helm of an agency who really does not have experience in that field,” said Intelligence Committee Chairman David L. Boren (D-Okla.).

For some key senators, however, doubts about the past translated into deep misgivings about the future of the CIA under the leadership of someone so closely associated with the Casey era.

Senate Majority Leader George J. Mitchell (D-Me.) argued that “reaching back into the Casey era and selecting as the new director Casey’s own deputy is precisely the wrong signal” to send to the CIA “at the beginning of a new era in intelligence gathering.”

Although overshadowed by the controversy that accompanied the hearings on Thomas’ nomination to the Supreme Court, the Intelligence Committee hearings were the most exhaustive and longest ever conducted by the panel. Thousands of documents were examined and testimony was taken from hundreds of witnesses.

The result proved to be less an indictment of Gates than of the political influence, mistrust and low morale that pervaded the CIA under Casey and kept it from forecasting such momentous changes as the collapse of communism in the Soviet Union, according to critics.

Sen. John Seymour (R-Calif.) voted for Gates. Sen. Alan Cranston (D-Calif.) was not present, but he had indicated earlier that he planned to support the President’s nominee.

Times staff writer Douglas Jehl contributed to this story.