Inter-University Research Institutes (IURIs) are supposed to be shared properties of the researchers of corresponding disciplines. The Institute of Nuclear Study (INS) affiliated to the University of Tokyo was the first IURI equipped with large scientific facilities. A newly found set of records, collected and archived by Hiroo Kumagai, a former professor of INS, gives us new insights and interpretation of the history of the INS and its successors. INS was designed to be managed democratically on the sole basis of the common will of all nuclear physicists in Japan (the autonomy of the research community). It conflicted with the principle of the autonomy of the university. It is shown that the conflict of the two different kinds of autonomy was one of the motivations to create a new, larger physics institute, the Laboratory for High Energy Physics (KEK). Because of this historical background, KEK and other newer IURIs could provide “virtual” autonomy for researchers, though they are formally the institutes operated by the government.