With the dissemination of its Innovation Strategy in 2002, the Canadian government further solidified its commitment to a knowledge-based national competitiveness strategy. Through the unfolding of a multi-million dollar Workplace Skills Strategy (WSS) agency, and the launch of two research agencies, the Canada Foundation for Innovation (CFI) and the Canadian Council for Learning (CCL), the federal government of Canada has expressed a clear interest in shaping knowledge generation and has established conditions for particular forms of knowledge production. In this paper we analyze the knowledge discourse of these intermediary agencies, and consider implications for higher education, particularly in terms of research support and program development. Using methods of critical discourse analysis, we examined the Calls for Proposals and general program descriptions of the CFI, WSS, and CCL, and found that programmatic discourses are conflicting and ambiguous in terms of research foci, partnerships, and roles of individuals and institutions.