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.