Based on two national surveys of Japanese faculty members, the purpose of this study is to analyze whether changes had occurred in key aspects of governance arrangements in both national and private universities in Japan from 1992 to 2017. This study focuses on the changing relationships between national universities and the central government and the internal governance and management style at institutional level, due to the application of new public management theory and market mechanisms to universities in Japan. The main findings show: (1) the changing trends of governance arrangements in Japanese universities did not seem to be more managerially-oriented and centralized in general between 1992 and 2017; (2) actual changes did not occur in some aspects of governance arrangements in Japanese universities; (3) changes in governance arrangements in private universities present a sharp contrast to those occurring in national universities. This research has important implications that the current governance patterns in Japanese universities should be improved, and top administrators should provide more competent leadership.