A federal judge says national security laws are not intended to shield intelligence agencies from embarrassment.

In his reasons for delivering a key ruling in the Maher Arar affair, Mr. Justice Simon Noel of Federal Court said there is a “genuine public interest” in openly dealing with the subject of torture of detainees, and the use of information gathered through force.

“Protection from embarrassment is not covered in our security laws,” Judge Noel wrote.

The long-awaited reasons for a judgment handed down almost two years ago explain why the judge approved release of disputed sections of a 2006 inquiry report into the overseas torture of Mr. Arar, an Ottawa electronics engineer.

In the same vein, the delay in publication of Judge Noel's reasons resulted from lengthy deliberations over what portions of his top-secret explanation could be disclosed. Portions of the judge's July, 2007, reasons remain blacked out.

It's the latest chapter in the long-running saga of Mr. Arar, a Syrian-born Canadian who was detained at a New York airport in September of 2002 and subsequently bundled aboard a private jet by U.S. authorities. He was flown to Jordan and driven across the border to Damascus, ending up in a crypt-like cell where he gave false confessions under torture about terrorist links.

An inquiry led by Mr. Justice Dennis O'Connor concluded in September of 2006 that the RCMP passed misleading, inaccurate and unfair information to the Americans that very likely led to Mr. Arar's arrest and transfer to Syria.

In early 2007 the Canadian government apologized to Mr. Arar and gave him $10.5-million in compensation.

Months later, as a result of Judge Noel's ruling, additional passages of Judge O'Connor's report became public over the objections of federal lawyers who argued their release could damage national security, international relations or the defence of Canada.

The new elements revealed that Canada's spy agency suspected, within two days of Mr. Arar's deportation, that the U.S. Central Intelligence Agency had shipped him somewhere to face possible torture.

The suspicion within the Canadian Security Intelligence Service was fuelled by knowledge of a pattern of cases in which American authorities would send terrorism suspects abroad for questioning in countries that paid little attention to legal niceties.

Jack Hooper, then deputy director of CSIS, said in an Oct. 10, 2002, memo: “I think the U.S. would like to get Arar to Jordan where they can have their way with him.”

In his reasons released Thursday, Judge Noel said he was not persuaded that disclosing Mr. Hooper's comments would harm Canada's interests with the United States.

“Such disclosure might upset some officials but any reasonable person must admit that such a statement reflects the realities of the time. It might embarrass some, but again, such embarrassment in itself does not constitute injury.

“There is a legitimate public interest to inform the public of such knowledge within CSIS, in order to be able to assess the work done by the agency at the time.”

Judge Noel ruled that some disputed information, including passages of Judge O'Connor's report referring to CSIS's knowledge and assessment of Mr. Arar, should remain secret.

However, because of Judge Noel's judgment it also emerged that Judge O'Connor found the RCMP used information from an unnamed country to help obtain search warrants against several people in January of 2002, part of a broader anti-terrorist investigation in Canada.

The Mounties didn't tell the judge who issued the warrants the country had a questionable human rights record, and undertook no analysis of their own to determine if the information had been obtained under torture.

Judge O'Connor also concluded the RCMP again included suspect evidence in an application for a wiretap warrant in September of 2002. The information came from an alleged confession by Ahmad El Maati, another Arab-Canadian who was interrogated in Damascus but later disavowed his statements, saying they were extracted under torture.

Kerry Pither, a human-rights advocate who has written about the incidents, said Judge Noel's reasons underscore that Canadian agencies made “a mockery” of the sometimes legitimate need for confidentiality of national security matters.

“They tried and tried and used it as much as they possibly could to shield themselves from public embarrassment.”

It's not the first time Judge Noel has sharply warned security officials against undue secrecy.

The judge made waves recently in the case of Mohamed Harkat, who faces deportation on a national security certificate. Noel expressed grave concerns about CSIS's failure to disclose important evidence about the reliability of an informant to the court.

As a result, hearings to determine the validity of the case against Mr. Harkat have been delayed for months.

Mr. Arar continues to wage a legal fight for redress in the American courts.

A separate federal inquiry headed by Mr. Justice Frank Iacobucci, a former Supreme Court judge, looked into the imprisonment of Mr. El Maati and two other Arab-Canadian men in the post-9-11 period.

In his October, 2008, report, Judge Iacobucci said Canadian officials shared responsibility for the torture of Mr. El Maati, Abdullah Almalki and Muayyed Nureddin in Syria through the sharing of information with foreign intelligence and police agencies.

The three men are seeking apologies and compensation.