Japan’s stringent university regulations were considerably relaxed after 1998. This paper’s analysis of Japan clarifies changes in the collaborations and interactions between universities, industries, and governments before and after this deregulation. A historical case study with the triple helix framework is applied; it uses the ‘triple helix’ for modelling the dynamics of university–industry–government relations. Most studies that use the triple helix model focus on university collaborations, while this study examines the whole range of university–industry–government collaborations. The results show that the collaborations which lead the development of university–industry–government relations, as well as the scope of collaborations, change in response to reforms in regulations. Industry–government collaboration led the development of university–industry–government relations before deregulation, and university–industry collaboration did so after deregulation. Though university–industry–government relations continue to develop, the scope of industry–government collaboration decreases because of deregulation. We interpret these factual findings in line with the triple helix model. We discover the characteristic development process of the triple helix model; it has a period wherein the triple helix develops under the prominent role of the government. Two possible reasons could be cited for this process: first, there were stringent regulations on university–industry collaborations; and second, industry–government collaborations were active through public-sector laboratories which were widespread in Japan.