Research of potential socio-economic value is commonly conducted within cross-sector (government, university, business) centres. Success depends on partners whose objectives and strategies may converge or compete. Yet little empirical evidence exists on: (a) how individual researchers perceive the benefits of their participation, (b) how far the structures and functions of particular collaborative R&D centres coalesce around of researchers' expectations and, (c) what problems arise for researchers who opt for a "second job" in the centre. The paper presents a qualitative analysis of a survey of respondents from public sector organizations involved in Australian Cooperative Research Centres. A novel frame for analysing these data is the study of inter-organizational relationships (IOR). We use the perspective of the individual research scientists to illuminate the important management issues of trust, governance, and competition between functional domains, which emerge from IOR and which have been inadequately recognised in the context of collaborative R&D centres. The findings have implications for the management and of the centres, for the careers of research scientists and for public policy.