As in many industrialized countries, Japan carried out a deregulation of higher education around the turn of the 21st century. This reform was based on New Public Management (NPM) principles, which should have been reflected in its most salient step: the incorporation of national universities in 2004. Although the way that the NPM principles were implemented in various countries was far from uniform, the Japanese version was no doubt quite peculiar. For example, from the outset, the management by objectives approach did not work well, due to deficits in the mechanism of ex-post evaluations. In addition, a roll-back of ministerial regulation emerged over time, under the guise of performance-based funding. As a result, universities rarely felt favored or promoted. Particularly in resource allocation among the institutions, they hoped for more transparency. It is assumed that this trend of re-regulation in the Japanese system will (in all likelihood) continue in the foreseeable future.