In a letter to Abousfian Abdelrazik's lawyer, a Justice Department official said his request for an emergency passport was rejected.
"We denied the passport on the basis of national security," Foreign Minister Lawrence Cannon said to reporters at the NATO summit in Strasbourg, France.
Mr. Abdelrazik has been trapped in the African country after his name appeared on a United Nations no-fly list.
There have also been allegations, which Mr. Abdelrazik has always denied, that he belonged to al-Qaida and had gone to a terrorist training camp in Afghanistan.
He has been cleared of terror ties by both Canadian and Sudanese authorities.
New Democrat MP Paul Dewar has been fighting to get the former Montrealer, who has an ex-wife and three children in Canada, freed.
"It's time to end six years of misery for this Canadian citizen and bring him home," said Mr. Dewar, who said federal officials recognized Canada's obligation to issue travel documents for Abdelrazik as recently as Dec. 23.
Mr. Dewar said Passport Canada stated it would issue a passport for Abdelrazik if a ticket was purchased for him. That airline ticket -- purchased for Mr. Abdelrazik with donations from almost 200 Canadians -- expired Friday.
"The only obstacle standing between Mr. Abdelrazik and his flight home to Canada is this Conservative government," Mr. Dewar said in a statement.
In a move designed to force Ottawa to get Abdelrazik out of Sudan, the NDP MP submitted a motion Friday to the foreign affairs and international development committee summoning Abdelrazik to appear.
Liberal MP Irwin Cotler said every day Abdelrazik spends in Sudan is another denial of his rights.
"This is a case where the Canadian government is alone directly responsible for the violation of the rights of a Canadian citizen that it is obliged to protect," Mr. Cotler said in a statement.