Public policy problems are socially complex due to a range of stakeholders who involve in the coordinated action. They are also often not stable due to situation changes or stakeholders’ behavior changes. Holistic thinking is actually required to solve a public policy problem, which is generally non-linear and highly complicated, through collaborative efforts across organizational boundaries. The approach of systems modelling offers an option for formulating and rehearsing strategic initiatives to resolve the problems in a systematic, structured and accountable. This paper presents an innovative effort to implement a triple helix model for supporting the development of national policies using systems modelling approaches initiated by the President’s Delivery Unit for Development Monitoring and Oversight (UKP-PPP) of Republic Indonesia and the School of Business and Management, Institut Teknologi Bandung (ITB). Series of workshops have been initiated to facilitate communication and cooperation among researchers in academic institutions, practitioners in industry and business, and decision makers in government. Analyzing this finding and interactions that occurred among stakeholders during the workshops, a model of Triple Helix interactions is formulated. In addition to known interaction between university and industry, interaction between university and government on policy development through the channel of state-owned research and development agencies was identified. Not only promoting systems modelling as a methodology in policy development, the workshops also provided evidence on the importance of having a holistic or systemic approach in formulating policies to address a complex national problem that requires interactions among stakeholders.