The Japanese manufacturing industry has sought to increase its international competitiveness by developing higher value-added products. Simultaneously, R&D that exploits external resources – as typified by open innovation – is also taking hold.Although collaborative product development research between public research institutions and private-sector companies is widely conducted, there are many instances when the results are not achieved due to differing perceptions of the partnership. Under such conditions, especially when the research is publically funded, methods for better managing the projects are being sought at the policy level. Using examples of publically funded industry-academia collaborative projects, this paper considers efficient management methods for projects aimed at such development.The research focuses on changes to the collaborative research system used in partnership projects and shows that it is more effective to conduct collaborative research that incorporates other companies as needed, without fixating on the original make-up of the collaborative system at the start.