The American Civil Liberties Union (ACLU) released newly obtained documents on Wednesday, one of which included a disturbing account of an interrogation in late 2002.
The commander of the US Southern Command, which is responsible for the prison at Guantanamo, immediately ordered an investigation into the FBI allegations of abuse.
"The Command wants to establish the facts and circumstances surrounding all allegations ... and consider the opinions and recommendations of an independent investigating officer," said Colonel David McWilliams, a spokesman for the US Southern Command.
One document describes how an FBI special agent (SA) observed a female interrogator caress a shackled prisoner, whisper in his ear and then cause him to grimace in pain.
"SA [name deleted] asked what had happened to cause the detainee to grimace up in pain," the document said.
"The marine said [she] had grabbed the detainees thumbs and bent them backwards and indicated that she also grabbed his genitals."
The document showed that the marine also implied that her treatment of that detainee was less harsh than her treatment of others.
He said he had seen her cause other detainees to curl up into a foetal position on the floor and cry in pain.
TJ Harrington, a deputy assistant FBI director, recounted the incident in a 14 July letter to Major-General Donald Ryder, the head of the army's criminal investigation command.
Harrington said that although the incident and two others were raised with Pentagon intelligence and general counsel officials at the time, he had no record they were "communicated to DOD (Department of Defence) for appropriate action".
One document said a detainee
showed signs of having gone mad
FBI agents, he said, have also observed dogs being used "in an aggressive manner to intimidate" a detainee in September or October 2002, and in November saw a detainee after he had been subjected to intense isolation for over three months.
"By late November, the detainee was evidencing behaviour consistent with extreme psychological trauma (talking to non-existent people, reporting hearing voices, crouching in a corner of the cell covered with a sheet for hours on end).
"It is unknown to the FBI whether such extended isolation was approved by appropriate DOD authorities," he said.
A theme of some of the other released documents was that the FBI had long opposed the military's harsher interrogation methods.
A 17 August e-mail to Harrington reported that some 26 agents at Guantanamo said they had observed some form of mistreatment, although not by FBI personnel.
But FBI General Counsel Valerie Caproni determined that only nine warranted a follow-up interview.
The remaining 17 were deemed to be "appropriate DOD approved interrogation techniques", the e-mail said.
The new documents were released on the eve of Senate confirmation hearings of President George Bush's choice for attorney-general, Alberto Gonzales.
Gonzales was the White House counsel who laid the legal foundation for aggressive interrogations of "war on terror" suspects.
"Mr Gonzales bears much of the responsibility for creating the legal framework and permissive atmosphere that led to the torture and abuse at Guantanamo and elsewhere," said ACLU executive director Anthony Romero, in releasing the documents obtained through a Freedom of Information Act suit.