As a key element in Australia's national innovation system, public sector organizations, such as universities and public-funded research agencies, have increasingly become involved in R&D collaborations with firms. Government policy has encouraged this cross-sector collaboration, and in the most recent policy "act" has focused on the commercialisation of research findings (through which R&D outputs are translated into marketable commodities) and has encouraged public sector organizations to become more directly involved in this activity. But while the policy rhetoric has contributed to a discourse of marketization, through which cultural change in the research performing organizations is both promoted and legitimised, there are other voices in the unfolding policy drama which point to the complex and multifaceted nature of commercialisation in national economies. These countervailing voices emphasise the multiple roles that public sector organizations play in national innovation systems, and this introduces organizational role ambiguity into the discourse leading to confusion among the research performing actors. It is concluded that, given the complex and subtle nature of innovation processes, the traditional dichotomy between applied (or commercially-focused) research and "public good" research is no longer tenable nor helpful in the policy debates.