High-level detainees such as Khaled Sheikh Mohammed and Ramzi bin al-Shibh, the September 11 ringleaders, are now in Guantanamo Bay in Cuba but there are still “ghost prisoners” among more than 6,000 who have been questioned by America and its allies since 9/11.

Their fate is among several unresolved issues raised by Bush’s new anti-terror legislation. His plans for military tribunals to try suspects are being held up by negotiations with leading Republican senators, including John Warner, chairman of the Senate armed forces committee, and John McCain, a favourite for the 2008 Republican presidential nomination.

McCain, who was a prisoner of war in Vietnam, insists that those accused should have access to the evidence against them and that torture should not be used. He is backed by Pentagon lawyers, who fear captured American soldiers will otherwise be vulnerable to mistreatment.

McCain’s position is irreconcilable with Bush’s, said Eugene Fidell, president of the National Institute of Military Justice. “Somebody is going to have to win and somebody is going to lose.”

Both sides are under pressure to come to an agreement so the spotlight can be turned on the Democrats’ supposed softness in the war on terror in time for November’s congressional elections.

Bush has offered no guarantees that the CIA will stop using what amounts to torture against new Al-Qaeda suspects. He told yesterday’s Wall Street Journal that measures to put his antiterror policies on firmer legal and political ground would benefit future presidents.

While the president said last week the CIA’s secret jails had been emptied, there remain “dozens” of important terrorist suspects who have “disappeared completely”, according to Clive Stafford-Smith, legal director of Reprieve, a UK charity that provides legal support for death row prisoners. “We know who is in Guantanamo, but where have the others gone?”

Reprieve believes many detainees are being held in a form of joint custody, where countries such as Afghanistan provide jail facilities and guards and the CIA supplies the interrogators. It says there are several hundred detainees still at Bagram airbase in Afghanistan, none of whom has been named by the Pentagon.

Among the “disappeared” is Ibn al-Sheikh al-Libi, who is said to have managed one of Osama Bin Laden’s training camps in Afghanistan. He was captured in 2002, questioned by the CIA and transferred under America’s programme of “extraordinary rendition” to a jail in Egypt. By 2003 he was back in CIA custody and was spotted by several prisoners at Bagram. Since then he has vanished.

Aafia Siddiqui, 34, a Pakistani educated at the University of Houston, disappeared in Karachi in 2003. American officials said she was under interrogation but, according to Reprieve, her family knows nothing of her fate.

Prisoners are thought to have been held in eastern Europe, north Africa and Thailand. A retired Jordanian general said last week that tens of American prisoners had arrived in Amman in unmarked jets and been questioned by Jordanian and American agents at the headquarters of the Mukhabarat, the Jordanian intelligence service.

Additional reporting: Uzi Mahnaimi and Bob Graham

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