The US has distanced itself from claims it captured “Al-Qaeda’s number three”, as secret files show information he gave about a radioactive bomb plot after he was tortured proved to be incorrect.

The disclosures add to concerns about the reliability of intelligence gained from detainees - who have either been tortured or given favours in return for information - and could help the case of Shaker Aamer, the last British resident in Guantanamo Bay who has been held for eight years without charge.

Last year, a Guantanamo detainee was released by a US judge after he ruled evidence from informants was not credible, and Mr Aamer’s lawyers said the only allegations he was involved in torture come from discredited informants, and statements made by Mr Aamer after torture.

The US claimed they had captured “Bin Laden’s lieutenant” and “the third or fourth man in Al-Qaeda” when they arrested Zayn Al Abidin Muhammed Husayn, also known as Abu Zubaydah.

A recently declassified document, titled CIA interrogation of Abu Zubaydah March 2001 – Jan 2003, said: “Abu Zubaydah was a senior lieutenant to UBL [Usama Bin Laden] (sic). At the time of his capture he was heavily involved in Al-Qaeda’s operational planning, and had previously been an external logistics coordinator.”

It also described him as one of the planners of the 9/11 attacks and the author of the “seminal Al-Qaeda manual on resistance to interrogation methods”.

Despite being seriously injured when he was shot twice during his arrest in late March 2002, the document reveal the US was interrogating him just days later, using waterboarding and sleep deprivation techniques - considered torture as defined by the UN Convention Against Torture.

“These enhanced interrogation techniques proved productive; Abu Zubaydah provided additional useful information,” the report noted.

“As of mid December 2002, Abu Zubaydah had been the source of over [next word redacted] disseminated counter intelligence reports.”

It stated: “Abu Zubaydah has corroborated intelligence on key Al-Qaeda planners and facilitators, and has and has provided information on Al-Qaeda’s CBRN [chemical, biological, radiological, or nuclear] program and on individuals associated with that program.

"Information from Abu Zubaydah was instrumental in the capture near Chicago of Jose Padilla, a ‘dirty bomb’ plotter, explosives expert and terrorist trainer and Qandahar. Abu Zubaydah also identified a senior Al-Qaeda operator.”

It continued: “Abu Zubaydah identified Jose Padilla and Binyam Mohamed as Al-Qaeda operatives who had plans to detonate a uranium-topped “dirty bomb” in either Washington DC or New York City. Both have been captured.”

Mr Mohamed, a British resident, was released from Guantanamo in 2009 after all terrorism charges against him were dropped. Allegations into his mistreatment are currently being investigated by police.

A US federal jury found Padilla guilty of charges that he conspired to kill people in an overseas jihad and supporting overseas terrorism, but neither man was charged with any offence relating to the dirty bomb.

In an August 2002, a memo sent from Jay Bybee, assistant Attorney General at the Department of Justice, to the CIA revealed how the US thought they had caught a “high value” terrorist in Zubaydah.

It said he was: “A high-value detainee - a top lieutenant with intimate knowledge of training and operations, a linchpin figure in many other terrorism cases.”

It continued: “According to this assessment, Zubaydah, though only 31, rose quickly from very low level Mujahedin to third or fourth man in Al-Qaeda. He has served as Osama Bin Laden's senior lieutenant . . . he also acted as Al-Qaeda's coordinator of external contacts and foreign communications.

"Additionally, he has acted as Al-Qaeda's Counterintelligence officer and has been trusted to find spies within the organisation.

"Zubaydah has been involved in every major terrorist operation carried out by Al-Qaeda. He was a planner for the Millennium plot to attack U.S .... and Israeli targets during the Millennium celebrations in Jordan.

"Two of the central figures in this plot who were arrested have identified Zubaydah as the supporter of their cell and the plot. He also served as a planner for the Paris Embassy plot in 2001. Moreover; he was one of the planners of the September 11 attacks. Prior to his capture, he was engaged in planning future terrorist attacks against U.S. interests.”

In a recent court disclosure, the US appeared to be distancing itself from Zubaydah’s importance, relegating him to “an affiliate of Al-Qaeda”.

It said: “Respondent [US Government] does not contend that petitioner [Zubaydah] was a “member” of Al-Qaeda in the sense of having sworn “bayat” (allegiance) or otherwise having satisfied any formal criteria that either petitioner or Al-Qaeda may have considered necessary for inclusion in Al-Qaeda. Nor is the Government detaining petitioner based on any allegation that petitioner views himself as part of Al-Qaeda as a matter of subjective personal conscience, ideology, or worldview . . . the Government has not contended in this proceeding that petitioner was a member of Al-Qaeda or otherwise formally identified with al-Qaeda. Instead, the Government's detention of petitioner is based on Petitioner's actions as an affiliate of al-Qaeda.”

The US now alleges Zubaydah was creating a terrorist operation of his own and “supported enemy forces and participated in hostilities” and “facilitated the retreat and escape of enemy forces” after the US invaded Afghanistan in November 2001, a claim his lawyers deny.

Brent Mickum said: “I strenuously deny he was an affiliate of Al-Qaeda. There is an extraordinary amount of evidence in the case that is improperly classified or otherwise protected from disclosure that belies the Government's assertion.”

He added: “Zubaydah provided his torturers with a great deal of information that was false that resulted in the expenditure of millions of dollars pursuing false leads. What this is, is a perfect example of the types of information you get when you torture people.”

The use of informants’ intelligence came under the microscope last year after a court case involving one alleged terrorist collapsed.

In February 2009 Del Quentin Wilber, of the Washington Post, reported one Guantanamo detainee, Yasim Muhammed Basardah, “was rewarded with his own cell, McDonald's apple pies, chewing tobacco, a truck magazine and other comfort items” for information.

He provided evidence needed “to continue detaining scores of alleged terrorists”, Del Quentin said, adding a court filing showed a military investigator wrote, in a 2004 report, Basardah's “credibility was in question with interrogators”.

In January 2009 federal Judge Richard J. Leon ordered the release of 21-year-old detainee Mohammed El Gharani.

“The case was built largely on the word of two informers, one of whom is identifiable in court documents as Basardah, according to a review of the records”, the Washington Post report said.

“Leon, who did not identify Basardah by name in his public opinion, wrote that government personnel had questioned the informer's credibility. The government has ‘specifically cautioned against relying on his statements without independent corroboration,’ the judge added. The credibility of the other informer, who has not been identified, was “undetermined”.

Clive Stafford Smith, of charity Reprieve, which represents many Guantanamo detainees, said: “Favours include having their own cell and watching porn movies. Not one single word these people say should be relied upon in court.”

The revelations have implications for the fate of a Battersea man, who remains the last British resident to be held in Guantanamo.

Evidence linking Mr Aamer to terrorism come from allegations made by informants who have been discredited in other detainee cases, his lawyer said.

The US alleges Shaker Aamer, who has now been held in the Cuban prison camp for eight years, was helping the Taliban when he was captured in Afghanistan in 2001.

The only evidence it has put forward to substantiate those claims comes from these informants and statements his lawyers claim were elicited from him by torture.

Despite never being charged with any offence, and being cleared by a US review board cleared him for release in 2007, the US has refused to allow him back to the UK.

Brent Mickum, who represents Mr Aamer, a father-of-four from Battersea who has indefinite leave to remain in the UK, said he was now “more convinced than ever” of Mr Aamer’s innocence.

Mr Mickum, who could not name the informants for legal reasons, said: “The vast majority of evidence comes from five informants all of whom were former or continue to be present prisoners at Guantanamo.

All have been discredited to one extent or another, but two of the informants are completely discredited and there testimony has been thrown out judges trying other inmate cases.”

The two completely discredited prisoners had provided evidence against “perhaps as many as 100 other prisoners”, he said.

“The two that have had their evidence thrown out by judges are responsible for the most significant allegations against Shaker Aamer.

“Some of the allegations offered by the two would be laughable but for the fact the matter is so serious.”

Mr Mickum would not confirm or deny Basardah was one of the informants in Shaker Aamer’s case.

“This only confirms my belief that Shaker is being held for reasons unrelated to the charges in the factual return,” he said.

“He is being held for what he knows, not what he is alleged to have done, and this is becoming increasingly clear.”