TORONTO - 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.

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.

Lawyer Barbara Jackman, who has represented several security certificate detainees over the years, called it a significant decision.

"It's the first time that I know of that a Canadian court has comprehensively dealt with the issue of whether our police and intelligence services can rely on evidence obtained by torture," she said.

"It's been an ongoing problem that hasn't been properly identified and now the courts are beginning to deal with it, so I think it's very, very important."

In a motion in Mahjoub's 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. Jackman, who represented Mahjoub when this case was argued in court but no longer is his lawyer, said she hopes this decision will have an impact on the practices of CSIS and the RCMP.

Both the Iacobucci inquiry on the torture of three Muslim-Canadian men overseas and the inquiry into Maher Arar's overseas detention and torture called attention to the problem of receiving information gleaned through torture, Jackman said.

"But those are commissions and while the government should pay attention to them, I don't think they did," she said.

"Now this is a court decision which has more weigh, in the sense that it's sort of directing them that they have to smarten up."

Mahjoub, married with three children, was initially released from prison 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.