The foundational problem of the relationship between university and government concerns the maintenance the government as a fomenter of knowledge produced by the university, without governmental interference in the university´s autonomy in management and research. The combination the studies about the university of the peripheral countries and of the advanced countries with the analysis of decision-making process enables us to build the instruments to verify how government creates constraints on the university´s autonomy. In the Brazilian case, the application of these instruments shows that, despite all the talk about governmental intervention in the university, it is the very research community, who has the support of the bureaucrats of agencies that support research, that dictates the paths of university autonomy.