"No, I don't [believe Iran's claims] ... we saw missiles being fired at the airline, and that, for me, raised all sorts of questions," Champagne said in an interview with the Canadian Broadcasting Corporation.
The minister added that Canada will continue looking into the incident and study all statements by Tehran on the issue to identify those responsible.
Earlier in the month, the Iranian military promised to prosecute those responsible for the crash before the one-year anniversary.
On 8 January, a Boeing 737 operated by Ukraine International Airlines crashed soon after departing from an airport in Tehran. Citizens of Iran, Canada, Ukraine, Afghanistan, Germany, Sweden, and the United Kingdom were among the 176 passengers and crew who died. Iran later revealed that its military had shot the plane down by accident, laying the blame on a human error. In October, Canada announced it would have its own forensic team to examine the evidence of the crash.