The Government's process of secret hearings for the deportation of terrorist suspects came under renewed scrutiny today after a barrister revealed that MI5 had offered contradictory evidence against two men.

The conflicting evidence only came to light because Andrew Nicol, QC, a special advocate in the Special Immigration Appeal Commission (Siac), was representing both men in separate hearings before the court, which meets behind closed doors.

The Home Secretary and Home Office lawyers were criticised for putting forward the evidence in a ruling passed down by Mr Justice Newman in May but only made public today.

In a "closed judgment" made in the case of MK, a suspected Algerian extremist who was deported to France last month, Mr Justice Newman said the "administration of justice" had been put at risk.

MK, 33, was arrested in 2004 because of his association with Abu Doha, an Algerian militant who has been charged in America in connection with the plot to bomb Los Angeles International Airport on December 31, 1999. Abu Doha has been described as Al Qaeda's chief recruiter in Europe.

Among the allegations made against MK, based on intelligence gathered by the British security services, was the charge that he let Abu Doha use his French passport to travel to Ireland in 1997 and the Netherlands the following year.

But during MK's secret hearing on May 19 this year, the Government withdrew the alleged passport violations after being shown evidence by Mr Nicol, who represented Abu Doha in a separate hearing relating to his deportation to the US.

In an addendum to the closed judgment for MK, which was released today, Mr Justice Newman wrote: "Had the coincidence of Mr Nicol’s instruction in both cases not occurred, the Commission would have been left to determine the question whether Abu Doha used the appellant’s passport, on a false basis."

"It is unnecessary to elaborate on the consequences which might have flowed had the Special Advocates not drawn the Commission’s attention to the existence of these documents."

Mr Justice Newman observed that the security services do not "establish an evidentiary trail" when preparing material for Siac cases and criticised the Home Office lawyers for not preparing their case more thoroughly.

Although he upheld the deportation of MK, Mr Justice Newman concluded: "There has been fault on the part of the Secretary of State for the Home Department... the administration of justice in the Commission is put at risk if failures in connection with disclosures of documents occur."

The human rights group Liberty called for a review into the use of intelligence in Siac cases as a result of the ruling: "Our worst fear has been realised when the Government submits flawed secret intelligence to a commission which will determine if people are to be returned to countries where they may face torture," said Shami Chakrabarti, the group's director.

"The Home Secretary has a duty to explain why the commission was misled and how this can possibly be prevented under these shadowy arrangements in the future."

Sixteen other Algerian nationals face Siac hearings to determine whether they should be deported after Britain agreed a "memorandum of understanding" with the Algerian Government that they will not be tortured or put to death.

The Home Office insisted that the mistake was exceptional and not the result of systemic problem: "Siac, with the assistance of the Special Advocates, has identified an oversight in the Secretary of State’s disclosure process in this case.

"That this resulted from an error is accepted and steps are being taken to ensure that this does not occur again. It is however an exceptional error and not due to any systemic failure."

MK, who was never charged with a crime, was deported to France on September 14. He took the Eurostar to Paris after voluntarily deciding to leave the country. He has dual French-Algerian nationality and faces no criminal charges in France.

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