The immigration minister also filed a motion to stay the judgment of Judge Anne Mactavish, whose ruling meant refugee applicants would once again have access to Canadian health care while they wait for a ruling on their cases in Canada.
The government give 13 grounds for its appeal, including the argument that the judge made several errors of fact.
In an interview with CBC News, the lead lawyer who won the case said the delay in filing the appeal, and the motion for a stay of judgment, means his team will have to scramble to prevent serious health problems among refugees from going untreated.
"If the matter is stayed there will be a delay and so there will be thousands of persons who should be getting coverage as a result of that order who will be denied that coverage for a longer period of time," said Lorne Waldman, who represents the group Canadian Doctors for Refugee Care.
"Justice Mactavish in her decision made it clear denial of health coverage is putting people's lives at risk."
Waldman also says his group will seek to expedite the appeal hearing in order to resolve the matter.