The operation, which encouraged physical coercion and sexual humiliation to obtain intelligence, was known to President George Bush and fewer than 200 operatives. It was approved by the national security adviser, Condoleezza Rice, according to the report. The programme was governed by the rules: "Grab who you must. Do what you want," a former intelligence officer told the magazine.
The article was written by Seymour Hersh, the Pulitzer-prize winning New Yorker reporter who exposed the abuse scandal in Abu Ghraib. It is sourced to unnamed former and current intelligence officials.
The Pentagon flatly denied his claims. "Assertions apparently being made in the latest New Yorker article on Abu Ghraib and the abuse of Iraqi detainees are outlandish, conspiratorial, and filled with error and anonymous conjecture," said a Pentagon spokesman, Larry DiRita.
The revelations came as the US military prepares to stage the first of a series of unprecedented public trials of the US guards allegedly involved in the Abu Ghraib abuse. On Wednesday, Specialist Jeremy Sivits will appear before an extraordinary court martial at Baghdad's convention centre. He is likely to plead guilty to the charge of abusing Iraqi detainees.
Crucially, though, Mr Sivits is expected to testify that senior commanders at the jail had no idea that prisoners were being brutalised, a statement that appears to bolster Mr Bush's contention in a weekend radio address that the abuse was "the actions of a few". Over the weekend, however, the six other defendants claimed they were merely obeying orders from higher up.
"Our defence says he was following orders and that he believed the orders were lawful," Guy Womack, a lawyer for Charles Graner, the US guard pictured next to a pyramid of naked, hooded Iraqis, told the New York Times yesterday.
In return for testifying against his former comrades Mr Sivits is expected to get a lenient sentence of a year in jail or less.
The last two weeks have seen Mr Rumsfeld fighting for his political career. Calls for his resignation prompted Mr Bush to reaffirm his support for the beleagured defence secretary. Following testimony before congress and a trip to Baghdad to rally morale last week, Mr Rumsfeld appeared to have weathered the worst of the crisis.
But when asked about the congressional testimony of Mr Rumsfeld and Stephen Cambone, his under secretary for intelligence, a senior CIA official told Hersh: "Some people think you can bullshit anyone."
According to the article, Mr Rumsfeld set up the secret access programme, which is subject to the most stringent defence department security, a few months after September 11. Known by several code names, including Copper Green, it sought to avoid legal barriers preventing intelligence agents from acting quickly in order to apprehend, interrogate or kill suspects. It emerged from frustration within the Pentagon that the hunt for terrorist suspects had been hampered by bureaucratic constraints.
The Pentagon regarded the programme as one of its most successful strategies in the war on terror in Afghanistan. With the Iraqi resistance growing and intelligence gathering failing, Mr Cambone decided to apply the programme to Iraq.
"They weren't getting anything substantive from the detainees in Iraq," the former intelligence official told Hersh. "No names. Nothing that they could hang their hat on. Cambone says, 'I've got to crack this thing and I'm tired of working through the normal chain of command. I've got this apparatus set up - the special access programme - and I'm going in hot.' So he pulls the switch, and the electricity begins flowing last summer. And it's working. We're getting a picture of the insurgency in Iraq and the intelligence is flowing. But we've got more targets [prisoners in Iraqi jails] than people who can handle them."
According to Hersh, Mr Cambone then decided to bring military intelligence officers into the prison alongside the military police guards, many of whom have featured in the abuse photos.
A Pentagon consultant who spent much of his career involved with special-access programmes told Hersh the blame goes beyond Mr Cambone. "The White House subcontracted this to the Pentagon, and the Pentagon subcontracted it to Cambone. This is Cambone's deal, but Rumsfeld and Myers approved the programme."
Mr Rumsfeld may not be personally culpable, the consultant added: "But he's responsible for the checks and balances. The issue is that, since 9/11, we've changed the rules on how we deal with terrorism, and created conditions where the ends justify the means."