In the 1950s, postwar Japanese scientists argued for the establishment of new re-search institutes that would pursue a democratic management of science. Their discussions led to the establishment of national inter-university research institutes (IURIs) for joint research activities, such as the Research Institute for Fundamen-tal Physics (RIFP) at Kyoto University and the Institute for Nuclear Research (INS) at the University of Tokyo. IURIs served as important joint research centers in various fields in postwar Japan. In the management system of IURIs, despite be-longing to the national universities, the scientists made up an organ reflecting the opinions of scientists across the country. In the initial stages, the IURI model seemed to work well as an ideal approach to the democratic management of sci-ence. However, in the case of INS, the system resulted in a conflict between scien-tists and the university, and the IURI system led to several serious organizational problems. The establishment of INS also faced difficult problems over nuclear research after the Bikini Incident in 1954.