Canada's national security agency does not have an "effective mechanism" for ensuring it does not rely on evidence obtained by torture, the Federal Court has found.

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Mohamed Mahjoub is shown in this undated family handout photo. ((Toronto Star/Canadian Press))

The court sided with a man accused of terrorist links, who Ottawa is trying to deport, in finding there are "reasonable grounds" to believe some of the information against him was obtained through torture and is therefore inadmissible.

Mohamed Mahjoub was arrested in 2000 and held on a national security certificate, accused of links to an Egyptian Islamic terrorist organization.

In a motion in his case he argued that the policy of CSIS to "not knowingly" rely on evidence from torture doesn't actually prevent it. The court agreed.

"In my view, these policies and practices do not provide for an effective mechanism to ensure that such information is actually excluded from the evidence," writes Justice Edmond Blanchard.

"It is also clear from the record that the service does not have the means to independently investigate whether the information is obtained from torture."

The court has ordered the government to review its information against Mahjoub and identify sources.

Mahjoub, married with three children, was initially released from prison and allowed to return to his Toronto home under conditions amounting to house arrest in 2007. However, he asked to return to prison after family supervising him said they could no longer deal with onerous conditions imposed by the court.

He was ordered freed again in November 2009 after a months-long hunger strike — during which he lost more than 50 pounds — to protest the conditions in the prison. Mahjoub was allowed to leave the holding centre in eastern Ontario as long as he wears a monitoring bracelet and honours other restrictions.

National security certificates are rarely used immigration tools for deporting non-Canadians considered a risk to the country.