Mohammed Harkat was arrested in 2002 and accused of being allied with Osama bin Laden. (Chris Wattie/Reuters)

A federal judge says Canada's spy agency may have disobeyed court orders by withholding information in the case of terrorist suspect Mohammed Harkat.

In a judgment released Wednesday, Federal Court Justice Simon Noel said he wants to review all evidence provided by CSIS and recall the agency's witnesses.

Calling it a "troubling situation," Simon says recent disclosures raise questions about whether CSIS has been operating in good faith.

The ruling comes on the heels of a top-secret letter sent to Noel from federal lawyers.

The letter contained information dating back to 2002 about the reliability of an informant who worked with CSIS.

The letter, prepared by counsel for Public Safety Minister Peter Van Loan and Immigration Minister Jason Kenney, acknowledged that the material should have been turned over earlier and that "failure to do so is a serious matter."

It added that CSIS was investigating to find out why the delay occurred and would provide more details to the court as soon as possible.

Judge sees 'possible prevarication'

Noel raised the possibility that CSIS witnesses have lied and that the agency may not have complied with court orders.

In his ruling, Noel wrote that the delay raises questions about the spy service's compliance with past court orders and about "possible prevarication" by CSIS witnesses who have testified before him.

Simon has ordered the government to produce its information by June 1 in complete, unrevised form to Paul Copeland and Paul Cavalluzzo, two security-cleared lawyers appointed to ensure Harkat gets a fair hearing.

He said to do otherwise would bring the administration of justice into disrepute.

Norm Boxall, one of Harkat's lawyers, called it an astounding judgment.

"It raises serious credibility issues with respect to the national security service and, as they say, it takes a lifetime to build a reputation and a minute to lose it," he said.

Boxall added it could lead to a stay of the government's entire case against Harkat.

CSIS said it is still trying to determine how it will be respond to Wednesday's ruling.

Harkat, who was arrested in 2002 and is accused of being allied with Osama bin Laden, has been living in Ottawa, subject to a security certificate, for 3½ years.

With files from The Canadian Press