The unions sued the Harper government after it decided in 2010 to close the old employment insurance account and transfer the $57 billion balance into the government's general revenues.
The Confederation des Syndicats Nationaux said the move was unconstitutional.
The court, however agreed with the federal argument that it had the authority to this because the matter was dealt with in a 2008 Supreme Court decision.
A lower court sided with the federal government, but the Quebec Court of Appeal overturned that and the government appealed to the Supreme Court.
The justices say the original judge in the case was right to dismiss the union suit because it was bound to fail.