This paper examines developments in the governance of science and innovation in Japan, with a particular focus on the recent ‘regionalisation’ of innovation policies and policy support for new university–industry linkages. The paper charts the emergence of national funding programmes, greater institutional autonomy and the promotion of regional diversity. The paper presents two case studies to show how different regions have responded to the policy initiatives. The research suggests that there has been some movement towards regional diversity and the emergence of nascent regional innovation systems. However, questions remain as to the development and potential of truly regional governance structures for science and technology and the role of universities.