Concerned US defence workers were told to keep quiet about the alleged abuse of Iraqi prisoners, memos obtained by a US civil rights group have revealed.
Allegations of abuse at Abu Ghraib have rocked the US military
Documents released by the American Civil Liberties Union also show that special forces officers ignored FBI fears over their interrogation methods.
FBI and Defence Intelligence Agency concerns were ignored or brushed aside by special forces, says the ACLU.
The ACLU obtained the documents under the US Freedom of Information Act.
A Pentagon spokesman said the US has a policy of "full disclosure" on allegations of abuse and the government "condemns and prohibits torture".
According to the memos, detainees held in Iraq often arrived at prisons, including Baghdad's Abu Ghraib jail, which was at the centre of allegations of systematic prisoner abuse, bearing "burn marks" on their backs.
The documents also shed light on a tense relationship between the US military hierarchy in Iraq and intelligence agents posted to the region.
Several documents detail specific concerns about the conduct of military personnel in Iraq.
One memo, from Vice Admiral Lowell E Jacoby, head of the Defence Intelligence Agency (DIA), describes how staff who complained about abuse were threatened, had their car keys confiscated and e-mails monitored, as well as being ordered not to leave the base or speak to friends or relatives in the US.
Another details an incident in which a prisoner was punched in the face by military personnel "to the point he needed medical attention".
Task force staff did not record the medical treatment and confiscated DIA photographs of the injuries, the memo says.
Both documents were dated 25 June 2004.
The ACLU disclosures follow reports that a senior FBI official complained in 2002 about "highly aggressive" interrogation techniques at the US camp at Guantanamo Bay.
"These documents tell a damning story of sanctioned government abuse - a story the government has tried to hide and may well come back to haunt our own troops captured in Iraq," Anthony Romero, executive director of the ACLU.
The Pentagon has said that at least eight major reviews and dozens of congressional hearings and briefings on the abuse issue have already been completed.
Seven US military police and an intelligence officer have been charged in connection with the abuse. One reservist has been jailed for his role.
The US military's interrogation policies have become a controversial issue in Iraq, Afghanistan and at the US internment centre at Guantanamo Bay, Cuba.
A number of documents released by the ACLU refer to Maj Gen Geoffrey D Miller, who was posted to Iraq to make recommendations on interrogation techniques.
Previously he served as head of Camp X-Ray, the Guantanamo prison, from October 2002.
Maj Gen Geoffrey D Miller was sent to Iraq from Guantanamo Bay
He was posted to Abu Ghraib in March 2004, shortly before accusations of the prisoner abuse, which was committed from October to December 2003, emerged.
According to an FBI email released by the ACLU, Maj Gen Miller "continued to support interrogation techniques [the FBI] not only advised against, but questioned in terms of effectiveness".
An e-mail to Thomas Harrington, an FBA counter-terrorism expert, details "somewhat heated" conversations with Pentagon staff, in which officials admitted that the FBI's less physical interrogation style had yielded similar results.
In another e-mail, dated December 2003, the FBI notes a "longstanding" opposition to some Pentagon interrogation techniques.
The sender requested that certain information "be documented to protect the FBI".