Since the mid‐1990s, Japan has instituted a series of policy reforms in order to encourage greater university participation in commercial activity. Using data from a survey of scientists in engineering and biomedical fields in Japanese universities, we find that there has been a significant increase in commercial activity during this period, in particular, links to small‐ and medium‐sized enterprises. We also find that scientists are increasingly considering business potential when choosing projects. However, we find little evidence of the increasing commercialization leading to barriers to access to research tools. We also find that, despite the growing importance of formalized university–industry ties, university–industry linkages continue to be dominated by informal ties and gift‐exchange.