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Foreign Affairs Minister Peter MacKay has refused a passport to Abdurahman Khadr for reasons of national security, even though a federal court judge ordered Ottawa to cease denying the former terrorism suspect his travel document.

“It's not only our national security, it's the national security of other countries,” a senior government official told The Globe and Mail Tuesday. “And it goes to the integrity and the responsibility that goes with carrying a Canadian passport.”

The 23-year-old Mr. Khadr, who is a Canadian citizen, was captured in Afghanistan in 2001 and was held for months as an “enemy combatant” by U.S. forces at Guantanamo Bay, Cuba. He was released in 2003, but only after he agreed to spy for the United States. He has never been charged with any crime; however, he had been denied a passport by the Canadian government.

On June 8, the Federal Court of Canada found that Mr. Khadr was entitled to the “fairness and legitimate expectation owed to all Canadian citizens” in terms of applying for a passport. Ottawa was told it had used dubious grounds to deny him a passport, and was ordered to cease doing so.

The decision by Mr. Justice Michael Phelan allowed Mr. Khadr to reapply for his passport, but stopped short of entitling him to a new one.

In the ruling, Judge Phelan suggested that Mr. Khadr could face some hurdles in his passport application since national-security considerations were written into passport law after his case came to light. Mr. MacKay has now denied that reapplication using the new rules.

The minister's decision amounts to a victory for the federal government in its decade-long legal battle with members of the Khadr family. Their links to al-Qaeda are by now well known.

The family first came to the attention of the Canadian public in 1995, when family patriarch Ahmed Said Khadr was arrested in Pakistan on allegations that he had bombed an embassy.

He publicly appealed for the Canadian prime minister's help when he was detained on suspicion of plotting a deadly bombing against the Egyptian embassy.

Abdurahman Khadr's parents had left Canada in the 1990s to raise him and his siblings in Taliban-controlled Afghanistan. For a time, the family even lived in the same compound as Osama bin Laden and his top lieutenants.

Yesterday, Mr. Khadr's lawyer, Clayton Ruby, expressed disappointment over Ottawa's decision.

“It seems unfair that the court would order the passport returned to him, and then for the government to issue one, but revoke it before they give it to him,” Mr. Ruby said.

“It's sort of, ‘Don't fight us, we're the government, we're not going to let you win.'”

The passport fight is just one of the many battles the federal government is waging against members of the Khadr family, most of whom returned to Toronto after U.S.-led forces ousted the Taliban regime in Afghanistan in 2001.

Omar Khadr, 19, remains in the U.S.-run Cuban jail, having spent the past four years there facing allegations that he had killed a U.S. soldier in Afghanistan. U.S. courts judged this summer that the legal regime at Guantanamo Bay is illegal, making it anyone's guess as to when Omar Khadr may actually face trial.

Sister Zaynab Khadr, 26, and brother Karim Khadr, 17, have lately appeared in a Brampton, Ont., court to lend emotional support to a group of Toronto terrorism suspects. The accused were arrested in June in connection with an alleged al-Qaeda-inspired truck-bomb conspiracy.

Last year, the RCMP seized Ms. Khadr's belongings as they launched an investigation into whether she wanted to spread al-Qaeda propaganda.

In 2003, Karim Khadr was shot and partially paralyzed when the Pakistani army finally caught up with his fugitive father and killed him.

Abdullah Khadr, 24, was jailed shortly after he returned to Toronto last winter. He has recently detailed allegations of torture in Pakistan, as he attempts to thwart a U.S. extradition bid, involving charges he bought and sold weapons in Afghanistan for al-Qaeda.With a report from Brian Laghi