This paper identifies what can be called the "paradox of interdisciplinarity" (Weingart 2000) in Australian higher education research governance and explores some of its constitutive dimensions. In the Australian context, the paradox of interdisciplinarity primarily concerns the proliferation of a programmatic discourse of interdisciplinarity in government reports and government policy and strategy documents, often tied to notions of innovation and applicability, parallel to the persistence or even reinforcement of modes of governance and associated mechanisms that almost exclusively rely on rigid discipline-based classification systems to evaluate and fund research. Two interrelated dimensions of this apparent paradox are discussed. First, the conceptions of knowledge that underpin the use of notions of disciplinarity as well as interdisciplinarity in Australian government reports and policy and strategy papers are analysed. Second, an analysis of the Australian research governance system and its underlying mechanisms is presented, as they pertain to interdisciplinary forms of research. On the basis of these analyses, it is concluded that there is a significant mismatch between the discourse of interdisciplinarity and associated conceptions of knowledge on the one hand, and current, relatively inflexible governmental research funding and evaluation practices on the other. It is finally proposed that the occurrence and perpetuation of such a mismatch in the Australian context can only be understood properly if placed in the context of a more general paradox of research governance, where a politically charged rhetoric of innovation conflicts with the actual trend toward an increasingly diminishing scope for the self-organisation of knowledge.