A number of countries with public higher education systems have implemented privatisation policies. In Japan, the national government introduced the National University Corporation Act (NUCA) in 2004 and changed the legal status of national universities from that of government-owned public institutions to independent administrative agencies. Its objective was to incorporate them, giving their presidents discretionary power and encouraging financial independence and autonomous administration. Applying McNay's models of university governance, this paper tracks three stages of university governance longitudinally from 1886, when Japan's modern higher education system was established, to reveal the historical roots of problems that the NUCA is meant to address. In addition, the effects of the NUCA over the first 6-year period (2004-2009) are examined based on data analysis. Its criteria for analysis are developments in the direction of financial, administrative and intellectual independence, accompanied by increased levels of transparency and public accountability.