The Conservative government "carefully crafted" changes to the national security certificate system that brought the rarely used tool for dealing with threats to Canada in line with the Constitution, says a federal lawyer.

As a Supreme Court hearing on the controversial certificate system began Thursday, federal counsel Urszula Kaczmarczyk said the 2007 reworking allowed Mohamed Harkat of Ottawa, accused of terrorist ties, to know the case against him.

The high court agreed last year to hear a challenge of the system from Harkat, an Algerian refugee who was taken into custody under a certificate in December 2002 on suspicion of being an al-Qaida sleeper agent. A revised certificate was issued in his case in 2008 after the secretive process was revamped to make it more fair.

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The person named in a security certificate – a means of deporting non-citizens suspected of being terrorists or spies – receives only a summary of the case against them, stripped of supporting details to protect sensitive intelligence sources and methods.

Harkat, 45, denies any involvement in terrorist activities.

Chief Justice Beverley McLachlin and her colleagues peppered Kaczmarczyk with queries Thursday as the federal lawyer recited chapter and verse of Harkat's case. At one point McLachlin reminded her the court was interested not just in his circumstances but in the validity of the overall certificate regime.

"You have to answer that or face the consequences," McLachlin said. "That's why we're asking you these questions."

The government contends the certificate process is consistent with the guarantee of fundamental justice under the Charter of Rights and Freedoms.

"The security certificate scheme provides a substantial substitute for full disclosure and allows the named person to know and respond to the ministers' case," says a federal submission.

"Mr. Harkat is not entitled to any particular process, only one that satisfies the principles of fundamental justice."

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About two dozen people gathered outside the high court Thursday to show their support for Harkat. Some carried signs, including one that read: "Stop Secret Courts."

Harkat spoke briefly before the court convened.

"I hope the Supreme Court is going to hear our side of the story and exonerate (me) at the end," he said.

"Secrecy doesn't take you anywhere anyway, if you really have something about me, just you know, charge me. Put it on the table and I can defend myself."

In revamping the system, the government introduced special advocates – lawyers with access to secret material who serve as watchdogs and test federal evidence against the person singled out in the certificate.

In their submission to the Supreme Court, Harkat's lawyers argue the process is inconsistent with the charter because it provides only rudimentary information about the allegations he faces.

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Almost 11 years after his arrest, the former gas station attendant and pizza delivery man "is still unaware of the substance of these very serious allegations," says the filing.

Harkat lives in Ottawa with wife Sophie and was recently allowed to remove an electronic tracking bracelet from his ankle. However, he must check in with authorities regularly.

Harkat's counsel say the special advocates do not make up for shortcomings in the certificate process, noting these lawyers are greatly restricted in what they can say about the case and cannot initiate their own investigations.

The Supreme Court will ultimately decide just how transparent the process should be when the government wants to resort to a certificate.

During a rare closed-door hearing Friday, it will also review key issues related to evidence in Harkat's case.

In April last year, the Federal Court of Appeal upheld the constitutionality of the security certificate system, but ruled that summaries of some 1990s conversations be excluded from evidence against Harkat because the Canadian Security Intelligence Service destroyed the original recordings.

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The ruling left both sides dissatisfied and each asked for a hearing in the Supreme Court.

Two other men – Mahmoud Jaballah and Mohamed Mahjoub, both originally from Egypt – could face removal from Canada in long-running certificate cases.