The passport is an internationally recognized instrument to verify identity and citizenship of an individual to allow for foreign travel, as you all know. In Canada, we don't guarantee necessarily the right to a passport. We have the right to mobility under section 6 of the charter, which grants Canadian citizens “the right to enter, remain in and leave Canada”. The courts have recognized that a passport is a very important instrument in doing those things.
However, there are circumstances where a passport may be denied that are reasonable; the purpose must be valid. In this case, we're talking about national security, which has been recognized as a sufficiently important objective such that a passport may be denied.