Commercialisation of research has increasingly become a desirable activity for many tertiary education institutions (TEIs) across the globe. There is now widespread recognition by all sectors of society that TEIs engagement with research commercialisation will help drive a nation’s innovation system and contribute to the needs of the economy and society. However, in recent times, the growing accountability agenda for research commercialisation has raised important challenges for TEIs. There are increasing concerns that TEIs have failed to achieve the desired results of research commercialisation (for e.g. Dahlstrand, 2008; Goldfarb & Henrekson, 2003; Salmi, 2009) as has been anticipated by both public and private entities. Predictably, a broad range of stakeholders are increasingly asking TEIs to justify the use of public resources and to provide a more thorough account of their research outcomes (Fielen, 2007; Gauthier, 2004). There also remains considerable uncertainty amongst TEIs as to the mechanisms by which they are able to leverage the intellectual abilities of their research staff, particularly, given the complex and long-term nature of the commercialisation process. This study draws on the theoretical perspectives of new institutional theory (NIT) and uses three New Zealand TEIs as case studies to explore how public TEIs identify and render accountability in the process of enabling commercialisation of research. Data was collected using a mixed method approach of interviews and a broad range of secondary documents and archival records that covered the period 2002-2010. The constructive-interpretive research strategy permitted the simultaneous selection, inductive analysis, and interpretation of contextual data in order to construct emergent themes arising from the real-life context of commercialisation. The study highlights a number of important findings. First, TEIs are embedded in a complex network of institutionalised relationships with normative and cultural-cognitive obligations towards enabling commercialisation of research. These relationships require careful management to help shape TEIs responses to select and use appropriate accountability mechanisms to enable and enhance commercialisation. Second, while research commercialisation has become legitimised in terms of nation building activities, the commercialisation agenda has been potentially undermined by a strong performance based research funding (PBRF) culture. As a consequence, commercialisation remains a marginal activity as TEIs strongly view accountability for research in terms of funding levels. In the main, TEIs do not consider returning value in terms of commercialisation as an obligatory part of accepting funding to support basic research. Finally, new public management (NPM) accountability with a focus on bureaucratic compliance fails to recognise the uncertain, complex, and long-term nature of the research commercialisation process. To avoid NPM tensions, TEIs have ‘decoupled’ from the technical requirements to render accountability for commercialisation performance. Consequently, this is causing legitimating behaviour in TEIs and in fact, accountability for research commercialisation seems to have become a ‘representational faithfulness’ to the rhetoric in the TEIs strategic documents. This research makes important contribution to theory, policy and practice. In regards to theory, the current research contributes through the application of new institutional theory (NIT) to two demanding fields of research and this is the first time NIT has been applied to examine public sector accountability within the context of enabling academic research commercialisation. A conceptual model of accountability has been developed identifying accountability obligations, management of accountability expectations, and discharge of accountability obligations. While most studies are ex post, this framework provides a three stage model to help examine ex ante and ex post accountability. In relation to practice, this study identifies the gap between rhetoric and reality of accountability that seems to have become a characteristic of the accountability environment within which public TEIs operate. While the rhetoric in strategic documents helps legitimise research commercialisation, the accountability practices of commercialisation are not thoroughly embedded, widely accepted, and effective as the rhetoric suggests. The study provides a model for enabling commercialisation of research that helps inform practice from early stage development of a research culture, to setting clear research targets in terms of PBRF goals, to finally establishing commercialisation initiatives. In relation to policy, this study identifies notable tensions between academic research and commercialisation. As a consequence, government needs to become more explicit in articulating its policy on research commercialisation so that TEIs move beyond identifying accountability simply in terms of PBRF goals. The study demonstrates that government policy needs to provide incentives to ensure that academic research and research commercialisation become two important roles of TEIs that complement and reinforce each other. The PBRF policy needs to be redeveloped to recognise research in terms of economic contributions and value adding activities leading to commercial outcomes. There is an urgent need for both government and TEIs to frame policy that encourages the development of a research culture within TEIs that remains sufficiently focussed on successful research commercialisation.