Updated

A Justice Department audit of terror interrogations at three military bases overseas concluded Tuesday that FBI agents refused to participate when detainees were questioned under harsh and potentially illegal methods.

The FBI clashed with the Pentagon and the CIA over how at least two top Al Qaeda operatives were interviewed, Justice Department Inspector General Glenn A. Fine found during a three-year investigation.

In part, that led to an August 2002 order by FBI Director Robert Mueller for agents to withdraw from interrogations during which coercive or extreme methods were used to get information from detainees, the audit concluded.

"The FBI agents observed the CIA use classified techniques that undoubtedly would not be permitted under FBI interview policies," according to a summary of the nearly 400-page audit.

Additionally, FBI agents raised concerns about military interrogators at the prison at Guantanamo Bay, Cuba, who allegedly used snarling dogs to scare Al Qaeda operative Muhammad al-Qahtani and kept him awake for daily and continuous 20-hour interviews. The rift between the FBI and Pentagon over those interrogations was reported to then-Attorney General John Ashcroft, but senior Justice Department officials later told investigators that "they did not recall that any changes were made at GTMO as a result."

GTMO stands for Guantanamo Bay.

Overall, the audit gives the FBI fairly high marks for its conduct in the sensitive area on terror interrogations, which have become a political and global flashpoint over whether the Bush administration knowingly allowed the use of tactics widely defined as illegal forms of torture.

The audit found that FBI agents "avoided participating in the aggressive or questionable interrogation techniques that the military employed," and it found no evidence that the agents abused terror detainees. In a few cases, FBI agents didn't always report abusive interviews or leave when they were ongoing, but auditors blamed that mostly on unclear guidance from FBI headquarters on how to confront military interrogators who were working under a different set of rules.

"While our report concluded that the FBI could have provided clearer guidance earlier, and while the FBI and DOJ could have pressed harder for resolution of FBI concerns about detainee treatment, we believe the FBI should be credited for its conduct and professionalism in detainee interrogations in the military zones and in generally avoiding participation in detainee abuse," the audit concluded.

In a statement, Mueller said his agents will continue to be trained and fully aware of FBI policy against participating in coercive interrogations.

"These individuals perform a vital function in dangerous environments in order to fulfill the FBI's post-9/11 mission to develop intelligence and prevent terrorist attacks," Mueller said.

Among the claims investigated were whether FBI agents saw military or CIA interrogators waterboard suspected terrorists, frighten them with military dogs or mistreat the Quran. Auditors found no evidence that FBI agents witnessed or were aware of CIA interrogators waterboarding senior Al Qaeda operative Abu Zubaydah — although the Bush administration has since acknowledged he was one of three detainees who were.

Waterboarding involves strapping a person down and pouring water over his or her cloth-covered face to create the sensation of drowning. Both the Pentagon and CIA prohibited its personnel from waterboarding detainees in 2006.

CIA spokesman Paul Gimigliano said the agency was working under Justice Department advice that the interrogation methods were legal at the time Zubaydah was waterboarded. He said those methods "have been employed only when traditional means of questioning — things like rapport-building — were ineffective."

In the case of al-Qahtani, believed to have been designated as an additional hijacker for the 2001 attack, military investigators in 2005 proposed disciplining the prison commander at Guantanamo Bay for abusive and degrading treatment. The tactics included forcing him to wear a bra, dance with another man and behave like a dog, the Pentagon report found. The recommendations were overruled and the prison commander was later cleared of wrongdoing.

On Tuesday, Pentagon spokesman Bryan Whitman said the Pentagon reviewed the Guantanamo matter extensively and found no evidence of torture. Whitman said he was unaware of any Pentagon actions that would have delayed the Justice report. He said there are often discussions about what portions of reports should be removed for classified reasons.

Jameel Jaffer, national security director for the American Civil Liberties Union, said the report "shows a failure of leadership on the part of senior FBI officials."

"Senior FBI officials knew as early as 2002 that other agencies were using abusive interrogation methods," Jaffer said. "The report shows unequivocally, however, that the FBI's leadership failed to act aggressively to end the abuse."