Barack Obama is preparing to name a former Bush administration who was heavily involved in some of the most controversial issues of that era, including illegal wiretapping and torture, as the new director of the FBI.

But the Obama administration will emphasise that James Comey, who was deputy attorney-general under Bush, was among a small group inside the administration who opposed wiretapping and the use of interrogation techniques such as waterboarding.

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Since leaving the Justice Department, Comey has been working as a hedge fund manager and lecturer.

Comey, 52, is set to replace Robert Mueller, who has headed the agency since the week before the 9/11 attack and is due to step down in September.

The expected nomination comes at a time when the agency is under siege on a series of issues ranging from seizure of the phone records of journalists to failure to follow-up on Russian warnings about the alleged Boston bomb attackers.

The White House has not officially announced Comey will get the nomination but it was first reported by NPR and confirmed by other media organisations.

Comey, a registered Republican, may find it easier to get through the Senate nominating process than if Obama had opted for a Democratic-leaning appointee.

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Earlier this year, Lisa Monaco had been touted in the media as a possible first female head of the FBI but she is instead staying as a White House counter-terrorism adviser. Her nomination would have risked becoming bogged down in Senate questions over the Benghazi killings.

The ranking Republican on the Senate judiciary committee in charge of the nominating process, Chuck Grassley, welcomed the prospect of having Comey in charge of the FBI, but warned that he would face questioning over his links with Wall Street.

In a statement, Grassley said Comey had a lot of experience of national security issues. “But, if he’s nominated, he would have to answer questions about his recent work in the hedge fund industry. The administration’s efforts to criminally prosecute Wall Street for its part in the economic downturn have been abysmal, and his agency would have to help build the case against some of his colleagues,” Grassley said.

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Comey, who was deputy attorney-general from 2002 to 2005 at a time of panic over terrorism in the wake of 9/11, became a hero for many liberals for standing up to senior Bush administration officials over wiretapping. At one point, he was involved in a dramatic encounter in a hospital ward in 2004, visiting the then ailing attorney general John Ashcroft, to ensure that Bush administration officials would not take advantage of his condition to get him to sign off on an extension of the wiretaps.

Testifying before the Senate judiciary committee in 2007, Comey said he had refused to the extension on constitutional grounds, and that Ashcroft, too, had reservations. Comey threatened to resign.

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“This was a very memorable period in my life; probably the most difficult time in my entire professional life. And that night was probably the most difficult night of my professional life,” he told the committee.

The day after the hospital encounter, George W Bush modified the wiretapping program to take account of Comey’s concerns.

During his time at the justice department, he also fought to stop waterboarding and other interrogation techniques being used at Guantánamo. His concerns are recorded in emails that were later published.

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His emails to Chuck Rosenberg, his chief of staff, in April and May 2005 show his opposition to the brutal interrogations being used.

After his stint at the Justice Department, he worked for Lockheed Martin and Bridgewater Associates, and then took up a teaching position at Columbia Law School. Before joining the Justice Department he held a prominent position as US attorney for the southern district of New York.

He was involved in a series of high-profile cases of white-collar crime, including the prosecution of Martha Stewart.

As an assistant US attorney in Virginia, he was involved in the investigation of the 1996 bombing in Saudi Arabia in which 19 US military staff were killed.

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