US Defence Secretary Donald Rumsfeld has been accused of personally authorising a secret programme that encouraged abuse of Iraqi prisoners.
President Bush has strongly defended his embattled defence chief
An article in The New Yorker magazine says Mr Rumsfeld extended a programme already in use in Afghanistan.
The operation encouraged coercion and sexual humiliation of Iraqi prisoners to gain intelligence, it says.
The Pentagon dismissed the claims as "outlandish, conspiratorial... filled with error and anonymous conjecture".
"No responsible official of the Department of Defense approved any programme that could conceivably have been intended to result in such abuses," a Pentagon spokesman said.
Meanwhile, the Washington Post reported on Sunday that army intelligence officers had devised a special plan to allow a Syrian prisoner at Abu Ghraib who was believed to have important information to be strip-searched and deprived of sleep.
Human Rights Watch legal adviser James Ross told the newspaper that the plan "clearly allows for a crossing of the line into abusive behaviour".
The New Yorker article was written by the distinguished American journalist Seymour Hersh, who first published the leaked secret report detailing abuses at Abu Ghraib, along with photos of prisoners being abused.
It quotes unnamed intelligence officials as saying the original programme gave blanket approval to kill or capture and interrogate "high value" targets in the war on terrorism.
The programme, Mr Hersh says, stemmed from frustrations about legal impediments to efforts to target al-Qaeda leaders after the start of US operations in Afghanistan in 2001.
According to Mr Hersh, it allowed commandos to carry out instant interrogations - using force if necessary - at CIA detention centres around the world.
Last year, Mr Rumsfeld and Stephen Cambone, his undersecretary for intelligence, expanded the scope of the programme and brought its methods to the Abu Ghraib prison near Baghdad, the article says.
Pictures of inmates being abused by American guards at the prison have sparked outrage in the US and beyond.
The latest pictures show detainees being threatened with dogs (AP Photo/Courtesy of The New Yorker)
Mr Rumsfeld and senior Pentagon generals have been grilled by congressional committees.
During the hearings, Mr Rumsfeld said that abuse had never been sanctioned by senior commanders, and that the few who had engaged in illegal interrogation methods would be punished.
Seven soldiers have been charged.
Mr Hersh's allegations were rejected by Pentagon spokesman Lawrence Di Rita soon after the article appeared on The New Yorker website on Saturday.
"This story seems to reflect the fevered insights of those with little, if any, connection to the activities in the Department of Defense," Mr Di Rita said in a statement.