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WASHINGTON — CIA and military interrogators bucked repeated warnings from the FBI that methods used to question terror suspects were in some cases “borderline torture” and potentially illegal, the Justice Department’s internal watchdog reported Tuesday.

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 terrorist attacks through 2004.

Fine’s report raises troubling questions about CIA and Pentagon interrogators whose use of snarling dogs, short shackles, mocking of the Koran and other abuses of detainees overseas appears to have overstepped what U.S. courts would allow in collecting evidence.

In the 2002 interrogation of al-Qaeda commander Abu Zubaydah, for example, an FBI agent at the scene “raised objections to these techniques to the CIA and told the CIA it was borderline torture,” Fine’s report noted.

At the detention center at Guantanamo Bay, Cuba, FBI agents in 2002 openly clashed with military interrogators bent on “aggressively” interrogating al-Qaeda operative Muhammad al-Qahtani by confronting him with agitated dogs and keeping him awake for 20-hour interviews daily.

“We found no evidence that the FBI’s concerns influenced DOD interrogation policies,” the report concluded.

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.

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.

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