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Mohamed Mahjoub, right, and his wife Mona Elfouli leave federal courts on Queen St. West after a hearing to ease the 24 hr a day surveillance they are under, taken in November 2008.Fred Lum/The Globe and Mail

Eleven federal lawyers and assistants have been ordered to step down from a long-running national security case in an unusual court ruling that stops short of staying the proceedings.

The order comes after the government inadvertently took confidential legal files belonging to Mohamed Mahjoub, who has been imprisoned or under house arrest for a dozen years based on secret evidence.

In reaching his decision, Federal Court Justice Edmond Blanchard decided to the banish the 11 Dept. of Justice lawyers and clerks "in the interest of ensuring public confidence in the administration of justice."

Judge Blanchard had harsh words for Ottawa's "negligent" conduct, saying the seriousness of the consequences "cannot be overstated."

Ottawa accuses Mr. Mahjoub, 51, an Egyptian citizen living in Toronto since 1995, of posing a threat to public safety. It first slapped him with a national security certificate in 2000.

The father of three, who remains under house arrest, has been fighting to clear his name, claiming abuse of process.

Last summer, government lawyers inadvertently took confidential files belonging to his legal team from a locked courthouse room.

Mr. Mahjoub's lawyers argued the document seizure had irreparably damaged his right to a fair process and violated his constitutional rights.

They said the government had breached two fundamental tenets of the justice system: solicitor-client privilege and litigation privilege.

Judge Blanchard agreed to a point — but refused to toss the proceedings despite finding the situation "an affront to fair play and decency."

He found the government had not examined the Mahjoub files in any detail.

Society's interest in seeing the case decided on its merits outweighs the prejudice to Mr. Mahjoub, the judge decided.

"The conduct of the ministers, although negligent, was unintentional."

Although he refused to stay the proceedings, Judge Blanchard did say Mr. Mahjoub can use the Charter breach related to the seized documents and the delay sorting out the mess caused in his ongoing battle to toss the proceedings as an abuse of process.

The government alleges he had high-level links to a terrorist organization in Egypt, which he fled in the mid-1990s.

Documents obtained earlier by The Canadian Press show Canada's spy agency conceded several years ago that most of its evidence was derived from sources linked to torture.

The government insists Mr. Mahjoub still has extremist beliefs and remains a threat to public safety despite having had no contact with former associates for 16 years.

Canada has been unable to deport him because of the likelihood he could be tortured.

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