The high court dismissed the leave-to-appeal application of the men, who allege the government is hiding behind Section 38 of the Canada Evidence Act, which allows information to be withheld for national security reasons.
They were appealing a ruling last year by the Federal Court of Appeal that sided with the government over keeping information about their cases from being released. As is usual, the high court gave no reasons for Thursday's decision.
"It would have given the court a very important opportunity to grapple with a troubling and contentious piece of Canadian law," said Alex Neve, head of Amnesty International Canada.
"This is just one more blow for three men whose effort to obtain some justice, accountability and compensation for the grave human rights violations they've endured has been denied and obstructed by the Canadian government at every turn."
A government inquiry under former Supreme Court justice Frank Iacobucci concluded in 2008 that Canadian officials were likely partly to blame for the torture of the three men.
The trio, Abdullah Almalki, Ahmad El Maati and Muayyed Nureddin, deny they are terrorists. All were abused by Syrian captors, while El Maati was tortured in Egypt as well.
Iacobucci concluded that Canadian officials passed on information about Almalki that was "inflammatory, inaccurate, and lacking investigative foundation."
Almalki said he was disappointed with the decision, but pledged to keep pursuing his lawsuit against the government.
"I'll keep on working for more disclosure and to have government officials held accountable," he said.
Thursday's ruling will mean that Almalki and his two fellow litigants will have a much harder fight to see documents related to the conduct of Canadian officials in their cases.
Neve said it is not too late for the Canadian government to change course and give the men the apology and compensation they deserve. By fighting the case in court, Neve said, the government is essentially telling them: "you want an apology, you want compensation, well you drag it out of us in court."
Neve urged the government to accept the recommendations of the Iacobucci inquiry because they were made by a respected one-time Supreme Court justice.
It wouldn't be the first time the government relied on the advice of a respected jurist.
Almost five years ago, Prime Minister Stephen Harper publicly apologized to Maher Arar, a Canadian citizen born in Syria, for what he then called his "terrible ordeal." The government paid Arar $10.5 million to compensate him for the year of torture and imprisonment he endured in Syrian jails between 2002 and 2003.
Arar, an Ottawa engineer, was arrested during a stopover at New York's JFK Airport in October 2002 and deported to Syria, where he was tortured.
A judicial inquiry by Justice Dennis O'Connor concluded in September 2006 that the RCMP gave misleading information to the U.S., which may have resulted in his rendition to Syria. He also found that Arar had no links to terrorist organizations.
Almalki spent 22 months in a Syrian prison after he was arrested in May 2002 on a visit to Damascus to see his ailing grandmother.
Almalki, also an engineer by training, still suffers the effects of his long imprisonment and torture. He lives in Ottawa but has not been able to return to work.
"After all these years, I'm still doing physiotherapy, still getting treatment, still all the terrible things related to memory, PTSD, depression, cognitive limitations, still extremely frustrating, and I'm still getting treated for it," he said.