Evaluation of research performance has significantly increased in importance, particularly in many emerging higher education systems. In Malaysia, the Malaysian Research Assessment (MyRA) was developed to evaluate the research performance of universities and Research Centres of Excellence (RCoEs). This paper reports on a participatory action research approach aimed at developing a new framework for measuring research performance of Malaysian RCoEs. The introduction provides the contexts leading to the development and adoption of the MyRA including the challenges and its appropriateness as a tool for evaluating the research performance of relatively smaller entities namely, RCoEs. A stepwise approach in developing an alternative system of assessment for RCoEs is then described, leading to a list of prioritised components and criteria for the newly proposed tool. Finally, some of the wider implications of the new assessment framework are discussed, including the applicability to other contexts, lessons learned, and the contribution to the literature.