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The case has been described as "riddled with discrepancies", and Margaret Beckett, the Foreign Secretary, appealed to General Musharraf earlier this year to halt the execution.
Now the President, who rejected clemency demands last year, has voiced his own doubts during talks with MEPs in Brussels.
At a meeting of the all-party European Parliament’s Friends of Pakistan group earlier this week, General Musharraf responded to concerns raised by the condemned man’s MEPs.
"You must understand that I have to work within the constraints of the law," he said. "But I am willing to find a solution to this case that goes over and above what the courts are able to do."
Amnesty International wants General Musharraf to keep a list of detainees and places of detention and to end the practice of illegal abduction.
The charity compiled its report, Human Rights Ignored in the War on Terror, using testimony from former detainees of the US military prison at Guantanamo Bay in Cuba and from the families of those who have disappeared.
An Amnesty International spokesman, Claudio Cordone, said: "Hundreds of people have been picked up in mass arrests, many have been sold to the USA as ’terrorists’ simply on the word of their captor, and hundreds have been transferred to Guantanamo Bay, Bagram Airbase (a US base in Afghanistan) or secret detention centres run by the USA."
Pakistan has supported the US-led global war on terrorism since it was launched by President Bush shortly after the September 11 attacks.
As part of this Islamabad has deployed some 80,000 troops along the border with Afghanistan to hunt down Taleban militants and al-Qaeda fugitives, thought to have sneaked into the rugged region after the Taleban fell in late 2001.
But Amnesty alleges that, in co-operating in the War on Terror, "the Pakistani government has systematically committed human rights abuses against hundreds of Pakistanis and foreign nationals".
"Hundreds of terror suspects have disappeared after being taken into custody, many by Pakistan’s intelligence services," said the report.
"A large number of war on terror detainees have been literally sold into US hands by bounty hunters who have received cash payments in return, typically $5,000," it added.
Amnesty International's UK Director, Kate Allen, said: "Whereas 'disappearances' were virtually unheard of in Pakistan before 2001, since the start of the 'war on terror' hundreds of people have been subject to illegal detention after arbitrary arrests by secret intelligence forces.
"In many cases there is evidence of the direct involvement of US operatives (CIA and FBI) in Pakistan's wave of 'disappearances' and other human rights abuses, including rendition and torture.
"Despite secrecy and official denials, it is clear that the road to Guantánamo starts in Pakistan. President Musharraf must come clean about Pakistan's 'disappearances'."
The report said that some 300 people -- previously labelled as "terrorists" and "killers" by the US government -- have since been released from Guantanamo Bay without charge, the majority to Pakistan or Afghanistan.
Many detainees remain unaccounted for, including a baby, a 13-year-old Saudi boy called Talha and other children and women, the report claimed.
Amnesty said that it hoped Tony Blair had raised the issue when he held talks with General Musharraf yesterday.
In his memoir, In the Line of Fire, General Musharraf has said that Pakistan had captured 689 al-Qaeda suspects, 369 of whom had been handed over to the US authorities.
"We have earned bounties totalling millions of dollars," the President says in his book. He said today that profits from the sale of his book will go to women's rights groups or poverty charities.
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