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Mohamed Harkat takes part in a press conference in Ottawa on Wednesday, April 25, 2012.Sean Kilpatrick/The Canadian Press

Canada's top court has upheld a tough anti-terrorism law aimed at deporting foreign suspects, ruling that its saving grace is the ability of judges to keep an eye out for unfairness.

"The discretion granted to designated judges is the crucial ingredient that allows the proceedings to remain fair from beginning to end," Chief Justice Beverley McLachlin wrote for a unanimous court decision about the federal security-certificate system.

It was a message, if an indirect one, to a Conservative government that has been trying to reduce judicial discretion in sentencing and has run into roadblocks from judges at all levels: Tough laws can stand if they preserve a judge's role in safeguarding fairness.

The ruling came after a 12-year battle by a former Ottawa pizza delivery man, Mohamed Harkat, whom the Canadian government declared a danger to Canada and a member of the al-Qaeda terrorist network in 2002.

However, Mr. Harkat may never be deported to his native Algeria because of the risk of death or torture there, and because the court has said the danger posed by people such as Mr. Harkat diminishes over time. Except for three years in prison, he has been living in the community, with his wife and mother at one point entrusted with keeping an eye on him.

Public Safety Minister Steven Blaney expressed satisfaction with the overall ruling, but the Canadian Council for Refugees and the International Civil Liberties Monitoring Group said it leaves in place a fundamentally unfair process that relies on secret evidence.

It was the first major test of a revamped immigration law meant to protect Canada from foreign terrorists and criminals. It was also a test of how the Supreme Court, with a majority of its members appointed by Prime Minister Stephen Harper, deals with the balance between protecting national security and maintaining civil liberties.

The law provides for public court hearings and secret ones. It was revised by a minority Conservative government in 2007 after the Supreme Court, then mostly made up of Liberal appointees, had struck it down over excessive secrecy.

In the earlier version of the law, the suspected terrorist was not permitted legal representation in the secret hearing – a fatal flaw, the Supreme Court had ruled. The court had pointed to the situation in Britain, where special advocates with security clearances were permitted to represent the suspects in the secret hearings, and the Harper government set up such a system.

The Harkat case, using a process for deporting terror suspects that long predates Sept. 11, 2001, was a veritable TV miniseries of ups and downs.

There were findings of abuse of process against the Canadian Security Intelligence Service, the country's civilian spy agency, over a failed lie-detector test of an informant that CSIS kept from Mr. Harkat's lawyers. There was the destruction of CSIS documents. And there was the first-ever secret hearing of the Supreme Court, at the request of the government. The court said Wednesday that the secrecy was unnecessary, and the hearing should have been held in public.

The ruling was released in the shadow of a public dispute in which Mr. Harper has accused Chief Justice McLachlin of trying to have an inappropriate conversation with him about a case. The Chief Justice and representatives of the legal community have said the charge is false.

Chief Justice McLachlin has often stressed the importance of a formal process of dialogue between the court and Parliament, but of late, with the court handing the government five crushing defeats since March, the dialogue has seemed one-way. In this case, Parliament had made changes to the law as proposed by the court in the 2007 ruling, also written by the Chief Justice, and it easily withstood a court challenge.

However, the court's ruling gave the government only some of what it wanted. The security-certificate system is imperfect, Chief Justice McLachlin said, and judges have the responsibility to use their discretion to keep the hearings fair for the suspected terrorists – and if not possible, to call a halt to the proceedings.