They have other sources, but many require matching funds from industry
The Canada Foundation for Innovation (CFI) (http://www.innovation.ca/index.cfm) provides funding mostly for infrastructure (e.g., large equipment, etc.)
the Networks of Centres of Excellence (NCE) (http://www.nce-rce.gc.ca/index.htm) funds partnerships between university, government and industry
Microsoft has a fellowship program for new faculty (http://research.microsoft.com/ur/us/nff/) for $100,000 a year for 2 years. It's open to US and Canadian faculty members. The ligibility requirements are as of the application year you must:
be in your first, second, or third year as a faculty member
be in your first faculty position
be no more than 6 years from the completion of your most recent PhD