Then-Deputy Attorney General James B. Comey, right, and FBI Director Robert Mueller during a 2004 press conference in Washington. (Mike Theiler/EPA)

The pending nomination of James B. Comey to be FBI director began on Thursday to reopen old debates over George W. Bush-era national security policies. And despite Comey’s well-publicized role in challenging some of the controversial practices, he has come under attack from civil liberties advocates.

One day after President Obama’s plan to nominate the former senior Justice Department official to run the FBI became public, the American Civil Liberties Union became the second civil liberties group to raise questions about Comey’s involvement in the Bush administration’s post-Sept. 11 anti-terrorism tactics, such as warantless surveillance and tough interrogations.

Comey “approved some of the worst abuses committed by the Bush administration,’’ the ACLU said in a statement that accused Comey of signing off on “enhanced interrogation techniques that constitute torture, including waterboarding.’’

Obama has strongly opposed such tactics, and the spectacle of his nominee reviving that debate added a twist to the coming confirmation process to replace Robert S. Mueller III as FBI director. Mueller has served 12 years in the post; the term is limited by law to 10 years, but Congress in 2011 approved Obama’s request to extend it two years.

People with knowledge of the selection process have said that Comey, a Republican, has been chosen as a show of bipartisanship. He would inherit an FBI still undergoing an enormous post-Sept. 11 transformation into an intelligence agency capable of preventing attacks such as the recent Boston Marathon bombings.

While the timing of his nomination is unclear, the White House is eager to get it before the Senate so that he can take over the bureau when Mueller leaves Sept. 4.

Comey, a former U.S. attorney in New York, is known for his genial manner and imposing 6-foot-8 frame. He did not return telephone calls Thursday. But some of his former Justice Department colleagues rose to his defense, calling him an inspiring leader whose hallmark is his integrity.

They pointed to the moment that thrust him into the public spotlight: his famous 2004 hospital-room confrontation with White House Counsel Alberto Gonzales and Bush’s chief of staff, Andrew H. Card Jr. The two White House officials were attempting to persuade Attorney General John D. Ashcroft, who was recovering from emergency surgery, to reauthorize a controversial warrantless domestic eavesdropping program.

Comey, who was acting attorney general in Ashcroft’s absence, had refused to agree to extend the program. When he learned that the White House was attempting to go around him and get the ailing Ashcroft to sign off on an extension, Comey rushed to George Washington University Medical Center, arriving just before Gonzales and Card.

In May 2007 testimony that riveted the Senate Judiciary Committee, a visibly uncomfortable Comey described the confrontation as “probably the most difficult night of my professional life.’’ He later wrote a resignation letter but did not send it.

Comey described the event as “an apocalyptic situation where I and the Department of Justice have been asked to do something that is fundamentally wrong.’’

Ashcroft declined Thursday to discuss the hospital incident but praised Comey, calling him “a rule-of-law guy. The Constitution really means something to him.”

David N. Kelley, who served as deputy U.S. attorney under Comey in New York and later became U.S. attorney, said that he “can’t think of anybody better to run the FBI than Jim.’’

“He’s going to be the moral compass for that institution,’’ Kelley said.

Patrick Fitzgerald, a former U.S. attorney in Chicago and longtime friend, called Comey “an innate manager. In a crisis, he’s almost like the baseball players who say they see the ball slow down and know when to hit it. He sees things more clearly and calmly than just about anyone I’ve ever met.’’

When he was deputy attorney general, Comey selected Fitzgerald to lead the investigation into the leaking of CIA officer Valerie Plame’s name, a probe that led to the conviction of Vice President Dick Cheney’s adviser Lewis “Scooter” Libby.

Comey was criticized by some in the administration for that appointment, and he also tangled with Bush officials over enhanced interrogation techniques.

In e-mails obtained in 2009 by the New York Times, Comey called some of the techniques “wrong” and “simply awful,” although, the paper reported, he approved their legality.

It was unclear Thursday if Comey’s battles during the Bush years would cause him problems with Senate Republicans. Sen. Charles E. Grassley (R-Iowa) praised Comey’s national security credentials but questioned his recent work for Bridgewater Associates, a Connecticut-based hedge fund with $75 billion in investments for clients that include universities and foreign governments.

Since leaving the Justice Department in 2005, Comey has worked in the private sector, including a stint as senior vice president and general counsel at Lockheed Martin. He now teaches national security law at Columbia Law School.

The expected nomination also received a mixed reception from the law enforcement rank-and-file. While Konrad Motyka, president of the FBI Agents Association, praised Comey’s “outstanding reputation” among agents, the Fraternal Order of Police withheld judgment. Jim Pasco, the organization’s executive director, said it was concerned about Comey’s efforts at the Justice Department to open civil rights investigations into police departments.

Comey was chosen over Lisa Monaco, a former assistant attorney general who became Obama’s chief counterterrorism adviser this year.

She would have been the first female FBI director. White House officials said Thursday that Obama was impressed with her response to the Boston bombings and wanted her to remain in her current post.

Comey was a candidate for the top FBI job when Mueller’s tenure first expired in 2011, but people close to him said Thursday that he removed himself from the running because the timing wasn’t right for him and his family.

Comey is known for his deadpan humor, and David L. Holmes, emeritus professor of religion at the College of William and Mary — Comey’s alma mater — on Thursday recalled spotting Comey on campus when he was deputy attorney general.

Holmes jokingly chided Comey. “Jim, a Republican?” he said.

Comey smiled, Holmes recalled. “Yes,” Comey responded. “But the right kind.”

Ed O’Keefe, Julie Tate and Scott Wilson contributed to this report.