Comey will replace Robert S. Mueller III, who is required to vacate his post as head of the FBI on Sept. 3.
The bipartisan vote, with two senators voting "present," came after Sen. Rand Paul, R-Ky., lifted his hold on Comey's nomination after the FBI briefed Paul on the domestic use of surveillance drones, USA Today reported.
Comey, 52, was deputy attorney general in the George W. Bush administration and later worked for Lockheed Martin and HSBC.
"Jim is a natural leader of unquestioned integrity," President Barack Obama said in a statement issued by the White House. "In the face of ever-changing threats, he has repeatedly demonstrated his commitment to defending America's security and ideals alike. With Jim at the bureau's helm, I know that the FBI will be in good hands long after I've left office.
"As welcome as today's vote is, however, the Senate still has work to do," Obama said. "Like the FBI, the Bureau of Alcohol, Tobacco, Firearms and Explosives is a critical law enforcement agency, and it has been without a confirmed director for far too long. I urge the Senate to swiftly confirm Todd Jones, my nominee to lead the ATF, so that he and his team can do their part to keep American families safe. As senators from both parties recognized today, we cannot allow partisan politics to get in the way of protecting the American people."
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