Releasing email messages obtained under the Freedom of Information Act, the American Civil Liberties Union (ACLU) said on Monday that one detainee was wrapped in an Israeli flag and some were shackled hand and foot in foetal positions for 18 to 24 hours, forcing them to soil themselves.
The ACLU said emails suggested inhumane interrogation methods were approved by Bush - a charge the White House vigorously denied.
The military operation at Guantanamo Bay has come under increased scrutiny as former prisoners have alleged they were tortured.
The Pentagon maintains it runs a humane operation there and investigates all allegations of abuse.
The email messages released by the ACLU include a report by an FBI agent who witnessed "numerous physical abuse incidents of Iraqi civilian detainees", including choking, beatings and placing lighted cigarettes inside ears.
One detainee, according to an email report, had been left in a room at near 100 degrees Fahrenheit (37.8 C) and had pulled out his hair during the night.
FBI officials are said to have
disapproved of US military tactics
Another detainee was interrogated while wrapped in an Israeli flag and bombarded with loud music and strobe lights, according to an FBI agent's account contained in an email posted on the ACLU website.
According to the email messages, FBI officials disapproved of the practice of military interrogators posing as federal agents.
Posing as FBI agents is not on a list of interrogation methods approved by Defence Secretary Donald Rumsfeld, Pentagon spokesman Bryan Whitman said. The Pentagon is investigating the allegations.
The White House denied a suggestion in an FBI email dated 22 May 2004, that Bush personally signed off on certain interrogation techniques in an executive order.
The ACLU's disclosures primarily comprise email messages between FBI officials whose names the government removed before releasing them.
The ACLU says there is a major
rift between the military and FBI
In several, the writers describe and criticise various interrogation techniques they said they witnessed at Guantanamo.
While military interrogators are performing much of the questioning at Guantanamo, the FBI and CIA also have operations there.
Anthony Romero, executive director of the ACLU, said the FBI documents continue to show the US government was "torturing individuals in some instances" and demonstrates a major rift between FBI agents and the military over proper interrogation techniques.
"There was real concern within our law enforcement community about whether we are torturing individuals," Romero said.
In other developments, a military review found a second Guantanamo prisoner wrongly classified as an enemy combatant, Navy Secretary Gordon England said on Monday.
He added the detainee would be released soon to his home country.
He would be the second freed under a military process instituted after the US Supreme Court ruled last summer that prisoners at Guantanamo could challenge their detentions through the US court system.
To bolster its case for each of the prisoners against any such challenge, the Pentagon set up tribunals to review circumstances of each man's capture to determine whether they were properly held.
Of the roughly 200 detainees already released, at least a dozen have reportedly returned to the battlefield. More than 300 additional cases are still being reviewed.
Separately on Monday, a federal judge in New York said he would deny a government request to delay a review of whether certain CIA internal files related to Iraq should be made public.
Judge Alvin Hellerstein's comments marked a victory for the ACLU and other groups seeking information about the treatment of detainees at Guantanamo and in Iraq.