I suspect when the Cdn cencus refers to "native speakers" it refers to a response to a question like, what is your "mother tongue" rather than one that makes some attempt to determine the level of proficiency. I believe it is an attempt to get a general idea of changes in the countries language profile (in particular the French-English mix) rather than be an accurate refection of languages spoken. I suspect the more local provincial estimate may make a more genuine attempt at doing an estimate from their contacts with local sources for info- though there is no accurate figures.

Personally, I know many French speakers who have a greater command of French than those classified as "native speakers" by Statistics Canada's Census-but would not be captured by the Census, as the first language they spoke was not French. It is likely a similar situation - though all one can do is speculate (from either angle) as only indirect numbers have been captured.