Canada is a federal country. Simply put that means there are two governments for every Canadian and those governments divide up the responsibility for governing between themselves. For most Canadians that means having a Federal and a Provincial government both of whom have authority to govern in different areas of life.
So, for example, in Ottawa there are two governments with power over peoples’ lives – the Government of Canada and the Government of Ontario. Both governments have independent authority and neither is superior to the other. So long as the governments legislate within their authority they are supreme. So, for example, the Government of Ontario has complete authority over municipalities while the Government of Canada makes criminal law. The rules of who has authority over what are set out in the Constitution.
Sometimes of course laws do conflict. So it could be that a municipal law – say relating to massage parlours – could conflict with criminal law. If there is a true conflict the Government of Canada’s law would govern. The test for when there is a conflict and what is a proper law within the scope of each government’s authority is very complex. Suffice it to say that in Canada provinces are very powerful and the Government of Canada cannot push around the provinces. Indeed, taken collectively the provinces may well be more powerful that the Government of Canada.
The Territories, like Nunavut, are not like the provinces and have no inherent jurisdiction under the Constitution. The Territories exist as delegates or agents of the Government of Canada. So we have a Commissioner in Nunavut rather than a Lieutenant Governor. This last point may seem minor but it shows the difference between the Territories and the Provinces. The Commissioner represents the Government of Canada – the ultimate authority over the Government of Nunavut. A Provincial Lieutenant Governor represents Her Majesty the Queen – and not the Government of Canada – because the Government of Canada is no authority at all over, say, the Province of Manitoba,
Canada’s Constitution gives the Government of Canada the authority to govern the Territories. Over the years many of the powers of the Government of Canada have been put in the control of the Territories themselves. Some suggest that the Government of Canada could, in theory anyway, exercise that authority directly and govern Nunavut from Ottawa if it so decided. In practice such an attempt would be legally and politically problematic at best.
Nunavut (along with each of the other Territories), has its own government in charge of things such as health care, education and the protection of human rights. Arguably the legislation creating Nunavut, the Nunavut Act, has a quasi-constitutional aspect. Certainly the Nunavut Land Claims Agreement is a land claims settlement and has constitutional protection. As a result, an attempt by the Government of Canada to repeal the Nunavut Act and govern directly would likely fail legally (not to mention politically!).