No. The various security clearances, the three main levels that exist, are basically standard across the board. If Mr. Bernier had a top secret special access clearance when he was the industry minister, it would have been allowed to pass along with him when he left.
The only thing that would have changed is the special access. The special access limits you to a need-to-know basis to see certain information that others might not see. In this particular case it might be possible--and again, this is to be confirmed--that somebody in the Department of Industry would be allowed to see certain information that is not allowed to be seen by someone in the Department of Foreign Affairs, and vice versa.