This paper explores how policy research institutions (or think-tanks) will be challenged to retain their objectivity on public policy issues regardless of their source of funds, in processes such as the APRM. Drawing from the Nigerian situation (with particular reference to experience under military government) while suggesting a more general application, this paper sets out to analyse the relationship between privately and publicly funded think-tanks and government, and the extent to which that relationship may change commensurate with the extent of government funding. It investigates the extent of the real or notional independence of think-tanks. Six key variable discussed require close analysis in order to understand the nature of the relationship between the institution's independence and its sources of funds.