General Michael Hayden, a former director of the National Security Agency (NSA), has been chosen to replace Porter Goss, who unexpectedly quit on Friday after only 18 months in the job.
The appointment of Hayden, barely 72 hours after his predecessor resigned has thrust the US intelligence community back into the spotlight.
Hayden, who was also the deputy director of national intelligence, will take over, pending congressional confirmation, at one of the most difficult times in the CIA's history.
Speaking at the White House announcement, Hayden addressed CIA employees who will have to adapt to another change in leadership at America's premier spy agency.
"To the men and women of the CIA, if I'm confirmed, I would be honoured to join you and work with so many good friends. Your achievements are frequently under-appreciated and hidden from the public eye."
But there was criticism from both Democrats and Republicans on the choice of appointing a military officer as head of a civilian spy agency.
Susan Collins, a Republican senator, said: "To send a signal of independence from the Pentagon, he may want to consider retiring from the Air Force."
Dick Durbin, a Democratic senator, called the appointment "troubling", saying "many Republicans and Democrats believe he is the wrong choice, at the wrong time".
Some have questioned whether Hayden will be able to provide the president with the independent voice he needs at the CIA and whether his allegiance to the Pentagon will hamper his new role.
"The appointment of General Hayden is the latest example of President Bush giving promotions to those who have led the greatest attacks on our Constitution and fundamental freedoms"
American Civil Liberties Union
During his tenure at the NSA, Hayden saw the creation of a warrant-less domestic surveillance programme aimed at intercepting communications between suspected terrorists outside the US and those within it.
The undertaking of that programme will certainly be raised during Hayden's confirmation hearings in Congress.
Anthony Romero, the executive director of the American Civil Liberties Union has already criticised the nomination, saying: "The appointment of General Hayden is the latest example of President Bush giving promotions to those who have led the greatest attacks on our constitution and fundamental freedoms."
Admiral Stansfield Turner, a former CIA director, said Hayden was qualified to head the spy agency but raised concerns on what role he played in the NSA domestic surveillance programme.
"By background, by training, by his experience he certainly is qualified to be the director of the CIA for our country but you have to worry about whether he has broken the law in his previous activities, and if so then he is not qualified."
John Negroponte, the national intelligence director, defended the choice of a military officer.
"I believe the president has selected the best person, civilian or military, to lead the CIA in this critical period."
He also cited Hayden's experience at the NSA adding that he expects "quite a bit of questioning about this issue" but believes that Hayden "will be prepared to answer any questions that might arise".
Some administration officials have been quick to play down the resignation of Goss and the nomination of Hayden, saying it is part of an overhaul being spearheaded by Josh Bolten, the new White House chief of staff.