Prosecutors stopped far short of pursuing charges against interrogators, however, after concluding that the Pentagon was ultimately responsible for policing the treatment of al Qaeda detainees who were being held in military prisons.
More than three years in the making, the audit issued by Justice Department Inspector General Glenn A. Fine generally praises how the FBI handled terror interrogations following the Sept. 11 terror attacks through 2004.
When al Qaeda terrorist Abu Zubaydah was captured - six months after 9/11 - the FBI took first crack at his interrogation. But, when the CIA concluded agents were merely getting "throwaway information" - the spies took over - using what one FBI official later called, "borderline torture," reports CBS News Correspondent Bob Orr.
Agents pulled out as FBI headquarters ordered them not to take part. But, Tuesday's report from the Justice Department's Inspector General makes it clear, FBI agents for several years witnessed wide-ranging abuses at three military lockups in Iraq, Afghanistan and Guantanamo Bay.
Agents repeatedly asked FBI headquarters for guidance, but didn't get it, as prisoners at Gitmo were threatened with growling dogs, had their thumbs twisted back and heads wrapped in duct tape.
While the Inspector General's report "...found no instances in which an FBI agent participated in clear detainee abuse..." it blamed the FBI for failing to give clear instructions to its agents in the field.
The split, pitting the FBI against the CIA and Pentagon, came to a head over the treatment of the so-called 20th hijacker Muhammad al-Qahtani. Qahtani is accused by the government of attempting to enter the United States in August 2001 to be a muscle hijacker on one of the planes used in the 9/11 attacks. He was turned away at the Orlando airport and not allowed entry into the country.
Fine's report raises troubling questions about CIA and Pentagon interrogators whose use of snarling dogs, short shackles, mocking of the Quran and other abuses of detainees overseas appear to have overstepped what U.S. courts would allow in collecting evidence.
At the detention center at Guantanamo Bay, Cuba, FBI agents in 2002 openly clashed with military interrogators bent on "aggressively" interrogating al-Qahtani by confronting him with agitated dogs and keeping him awake for continuous 20-hour interviews daily.
"The plan was to keep him up until he broke," the FBI agent told superiors, the Justice Department report said.
FBI officials complained to the White House after learning that military interrogators forced al Qahtani to "perform dog tricks," "be nude in front of a female," and wear "women's underwear on his head".
Al-Qahtani's attorney, Gitanjali Gutierrez with the Center for Constitutional Rights, says that Qahtani recently attempted suicide in his cell at Guantanamo Bay because of his conditions.
"The tactics that were used against and the impact, the pain and suffering it caused him and the damage that it caused him does rise to a level of torture," Gutierrez told CBS News.
The treatment of al-Qahtani recently forced the government to drop the charges against him, because had the Pentagon proceeded with his military tribunal, all of the evidence of his treatment would be made public.
For at least part of the time covered by Fine's investigation, the CIA and Pentagon were working under Justice Department guidance that their interrogation methods were legal. However, FBI agents recognized as early as 2002 that they would not be allowed to use those methods to interview prisoners in the United States.
FBI agents are explicitly banned from using brutality, physical violence, intimidation or other means of causing duress when interviewing suspects. Instead, the FBI generally tries to build a rapport with suspects to get information.
"Beyond any doubt, what they are doing (and I don't know the extent of it) would be unlawful were these enemy prisoners of war," one agent wrote back to FBI headquarters in a document cited in the Justice report.
Fine's investigators found no evidence that FBI agents witnessed or were otherwise personally aware of cases where terror suspects were subjected to waterboarding, a particularly harsh interrogation tactic that critics call a form of torture. The CIA has acknowledged waterboarding Zubaydah, in part out of concern that he had information that could prevent another imminent attack.
Such tactics "have been employed only when traditional means of questioning - things like rapport-building - were ineffective," CIA spokesman Paul Gimigliano said Tuesday.
In al-Qahtani's case, Pentagon spokesman Bryan Whitman said no evidence of torture has ever surfaced after extensive internal reviews. Al-Qahtani, designated as an additional hijacker for the 2001 attacks, was forced to wear a bra, dance with another man and behave like a dog while at Guantanamo Bay, according to a 2005 Pentagon report.
Whitman also said he was unaware of any Pentagon actions that would have delayed the Justice report. Fine's audit, however, describes seven months of foot-dragging and negotiating by the Pentagon over how much information in the report should be classified or otherwise shielded from public review. The 438-page report issued Tuesday is only sparsely blacked-out.
The report surveyed over 1,000 agents, interviews with hundreds of other witnesses and a review of more than a half-million documents. It concluded FBI agents in nearly all cases refused to participate in harsh interrogations and left the room when they were ongoing.
Agents also were fairly vigilant about reporting their concerns to their superiors, the report shows.
At Guantanamo Bay, two FBI agents "had concerns not only about the proposed techniques but also about the glee with which the would-be (military) participants discussed their respective roles in carrying out these techniques, and the utter lack of sophistication and circus-like atmosphere within this interrogation strategy session," the report found.
Still, the FBI did not emerge unscathed in the report.
Auditors found that agents in a few cases did not always report the harsh tactics and in a few cases remained throughout the interrogations. Fine's office blamed the lapses on unclear guidance from FBI headquarters on how agents should confront interrogators who were working under rules dictated by the CIA or Pentagon.
In August 2002, FBI Director Robert Mueller ordered agents to withdraw from interrogations during which coercive or extreme methods were used to get information from detainees. But identifying or defining coercive behavior proved difficult for FBI agents who also wanted to get information from terror suspects, and who were assured by their counterparts that the methods were "approved at the highest levels," the report found.
Critics said senior FBI and Justice Department officials should have done more to stop the abusive interrogations.
"While I take comfort in knowing that, for the most part, FBI field agents followed the agency's policies regarding interrogations, I find it very disturbing that many senior FBI and DOJ officials failed to take strong action after identifying interrogation abuses," House Judiciary Committee Chairman John Conyers, D-Mich., said in a statement.
Mueller said his agents will continue to be trained and fully aware of FBI policy against participating in coercive interrogations.