It admits that FBI agents did "use techniques that would not normally be permitted in the United States or participate in interrogations during which such techniques were used by others", but said they did so "in only a few instances".
For the most part, the report says, FBI agents avoided participating in detainee abuse and many denounced any abuse that they witnessed.
The report adds that techniques used in Guantanamo and elsewhere included sleep disruption, prolonged shackling of hands and feet or wrapping a detainee's head in duct tape.
A female interrogator also grabbed a detainee's genitals to inflict pain.
From 2001 and 2004, the FBI sent more than 200 agents to Afghanistan, 500 to Guantanamo Bay and 260 to Iraq.
"Ultimately, neither the FBI nor the DOJ had a significant impact on the practices of the military with respect to the detainees," it said.
The 370-page report, however, details clashes between the FBI and the Pentagon over some cases, including over the interrogation of Abu Zubaydah, allegedly a senior al-Qaeda leader.
Human rights groups have called for
the closure of Guantanamo Bay [EPA]
There were also strains over Mohammed al-Qahtani, who was held at Guantanamo Bay, and has been described as the alleged "20th hijacker" in the September 11 attacks on the US.
The report quotes an FBI agent as objecting to Abu Zubaydah's treatment as "borderline torture".
The CIA has acknowledged Abu Zubaydah was one of three suspects subjected to waterboarding, which simulates the sensation of drowning, but the report said the information regarding interrogation techniques used on him were classified.
Al-Qahtani was subjected to sleep deprivation, loud music and extremes of temperature during sessions lasting 20 hours a day, according to a 2005 account of his interrogation.
The Saudi suspect tried to kill himself at Guantanamo last month, his lawyer said on Tuesday, saying he was distraught over a possible death sentence for charges later dropped by the Pentagon.
US officials did not explain why the charges were dropped and said they could be filed again later.
Robert Gates, the US defence secretary, has said that efforts to close the Guantanamo camp were "stuck" as many of the remaining prisoners' home countries had refused to accept their return or could release them and that there were further difficulties over transferring them to US prisons.
At Guantanamo on Wednesday, an Afghan detainee was dragged from his cell to his first tribunal hearing.
But Mohammed Kamin refused to participate, telling the judge he felt "helpless" and joining a growing number of detainees boycotting their tribunals.
Kamin had refused to leave his cell for his first appearance on a charge of providing material support for terrorism.
He is accused of placing missiles near US-occupied areas in Afghanistan.
"The trials are yours, the courts are yours. How can I trust you? I don't expect anything good from you," Kamin said through a Pashto translator.
"I am helpless. You have the force."
Kamin is the second prisoner to be carried out of his cell for a first appearance at the Guantanamo military tribunals, which have been condemned as unfair by human rights groups.