The Government is refusing to issue passports to two of the Britons released from Guantanamo Bay last month under a rarely used law, it emerged today.

Charles Clarke, the Home Secretary, used powers under the Royal Prerogative to deny passport facilities to Martin Mubanga and Feroz Abbasi, the BBC Radio 4 Today programme said.

It is not known whether the other two British detainees, Richard Belmar and Moazzam Begg, have also been refused passports under the powers, which have only been used 13 times since 1947. The last time they were invoked was in 1976.

The Home Office’s letter to Mr Mubanga, a 32-year-old former motorcycle courier from Wembley, north London, who was arrested in Zambia and sent to the US base in Cuba, said that the Home Secretary has the power to refuse passport facilities "if past or proposed activities were so demonstrably undesirable that the granting of the passport would be contrary to the public interest".

The letter said: "I’m writing to inform you that on the basis of the information which has come to light during your detention by the United States, the Home Secretary considered there are strong grounds for believing that, on leaving the UK, you would take part in activities against the UK or allied targets.

"We therefore decided on January 24 to withdraw your passport facilities for the time being. We further considered that the removal of passport facilities in preventing you from leaving the UK was a proportionate measure."

Mark Oaten, the Liberal Democrat home affairs spokesman, questioned whether Mr Clarke took the decision as part of a deal with the US to free the men. He said: "I would be extremely concerned if the Home Secretary had taken this decision based on some promise given to America.

"We were told that there were no conditions and, if it now emerges that there were, this raises serious questions. Surely the Home Secretary should take this decision himself - not part of a promise to appease the Bush administration?"

Mr Oaten demanded assurances that the evidence used to reach the decision was not gained through torture.

"We want absolute categoric assurances that the evidence... was not gained from Guantanamo Bay under torture," he told Today. "The power should only be used under absolutely extreme circumstances and I find it hard to believe that these conditions have been met this time."

Mr Mubanga claims that during his 33 months at Guantanamo Bay he was interviewed for hours, chained by the hand and ankle, and taken to "hot rooms" where the heating was turned up to around 40C.

He was immediately arrested on his return to Britain and questioned by anti-terrorist police officers before he was released without charge.

Explore UK News

• Crime News

• Education News

• Health News

• Science News

• Scotland News

Times Recommends

• DIY video helps the WI get to grips with sex
• Artists urge nation to save Titians
• Go home, Iraqi leader tells Britain