This could become an issue during Philip Mudd's confirmation hearing, which is expected next week. Mudd was nominated to be under secretary of intelligence and analysis at Homeland Security.
The aide confirmed that Mudd, who was deputy director of the Office of Terrorism Analysis at the CIA during the Bush administration, had direct knowledge of the agency's harsh interrogation program. The aide, who spoke on condition of anonymity, was not authorized to discuss the matter publicly.
A Republican senator wants more information about Obama's top pick for the post. Sen. Susan Collins, R-Maine, said her staff is looking into the extent of Mudd's involvement in these interrogation programs.
Neither Mudd nor the White House responded to requests for comment.
The interrogation program has come under harsh criticism by Democratic lawmakers and President Barack Obama.
Mudd's analysts used information obtained through harsh interrogations, and the official said that Mudd is likely to be questioned on whether the analysis branch pressured interrogators in the field to use harsher methods because they believed detainees were not telling the truth.
The Democratically controlled Senate will then have to decide whether indirect involvement or knowledge of the program is enough to disqualify a candidate that has been praised by several current and former intelligence officials.
In November, Obama's selection of John Brennan to become CIA director was derailed after a firestorm of criticism from liberal bloggers that associated him with the Bush administration's interrogation, detention and rendition programs.
Faced with the prospects of contentious confirmation hearings, Brennan withdrew from consideration. He currently serves as the president's White House-based homeland security adviser, a position that does not require Senate confirmation.
The date of Mudd's confirmation hearing before the Senate Select Committee on Intelligence has not yet been set.