The commissioner's authorities are based on the French Language Services Act. The commissioner's role is to monitor the application of the act. However, the commissioner's position—this was also the case in the old system—isn't under the aegis of the Ontario Ministry of Francophone Affairs.
As in the case of the auditor general or ombudsman, the commissioner is an independent officer of the Legislative Assembly of Ontario. As such, the position falls under the Legislative Assembly. I know that this can be confusing. At the legislative level, the commissioner obtains a mandate from the French Language Services Act. However, as a senior public servant, the commissioner reports to the Legislative Assembly of Ontario.
Regarding the transfer of the commissioner position, the final version of Bill 57 of the Legislative Assembly of Ontario, which amended certain statutes, clearly states that the French Language Services Commissioner remains a commissioner position, but under the auspices of the Office of the Ombudsman. As a result, the commissioner's related authorities remain the same.