After Mohammed's capture in Pakistan in 2003, the CIA detained him at one of several secret overseas prisons, known as "black sites," and subjected him to unusually harsh treatment, according to the article.
It was under these interrogation methods that Mohammed confessed to 31 criminal plots, including the murder of Wall Street Journal reporter Daniel Pearl, who was captured in 2002 in Pakistan and beheaded, Jane Mayer reports in the New Yorker.
Mohammed's interrogation was part of a fine-tuned CIA protocol of psychological coercion against al Qaeda figures, according to sources familiar with an International Red Cross report, Mayer writes.
"The Red Cross went in and got to interview these people for the first time," said Mayer on the CBS Evening News. "What these people described was hanging from the ceilings by their arms and being water-boarded, partially drowned, put on leashes and knocked into walls and basically deprived of all kinds of sensory imagery for years."
At a hearing in Guantanamo Bay, Cuba, Mohammed said his testimony was freely given, Mayer adds, but he also said that he had been abused by the CIA.
"He was certainly coerced," Mayer told Russ Mitchell on Sunday. "These were certainly very coercive techniques. The problem with them is that you can't really tell what's reliable, what's the truth, what's not after somebody has been through these things."
Mayer's article further described the CIA program of physical and psychological abuse as completely regimented and deliberate.
"There have always been mistakes made in the past when prisoners have been abused in wars," Mayer told Mitchell. "But this is the first time it's been done on purpose."
The program was suspended last fall, following a Supreme Court ruling, Hamdan v. Rumsfeld, which ruled that all U.S. detainees must be treated in a manner consisted with the Geneva Conventions.
In an E-mail to CBS News the CIA responded that the article "recycles old allegations" and concluded by saying "the United States does not conduct or condone torture."