Yes.  There are a number of different regulators of charities.  If a charity is a registered charity with the Charities Directorate of the Canada Revenue Agency, which is part of the federal government, then that registered charity is subject to the rules and regulations of the Income Tax Act that apply to registered charities.  CRA regulates organizations by determining which of them can have registered charity status, by revoking registered charity status of charities that do not comply with the rules and spot auditing charities to check compliance.  CRA educates charities about their obligations, including filing an annual return, restrictions on political and business activities and other matters.  As well the Canadian Department of Finance is responsible for the Income Tax Act and its regulations and amendments to the Act.  If there is a dispute between the CRA and a charity then it may go to court in which case the courts determine the outcome.

As well charities that operate in a particular province are subject to the jurisdiction of the public guardian and trustee of that province.  Ontario is the only public guardian and trustee that is active in regulating charitable activities.

Other government departments are also involved with regulating charities.  For example if charity is incorporated it is subject to the rules of the incorporating statute.  Therefore an Ontario non-profit corporation must look in part to the Ontario Corporations Act.  Different types of charities are subject to sectoral regulation – for example universities, hospitals, daycares etc.