ISSP belongs to the University of Tokyo. At the same time, its facilities are open to all domestic researchers participating in joint research. The administrative decisions are made at the faculty meeting chaired by the director and attended by professors and associate professors. The ISSP Advisory Committee, consisting of nearly equal numbers of members from and outside of the University of Tokyo to represent the interest of the outside users, gives advice on various aspects of administration upon inquiry of the director. The Advisory Committee for Joint Research, consisting of both the in-house and outside members, evaluates proposals for joint research, workshops, and allocation of fund for user activities.

  Currently ISSP consists of five Research Divisions, four Research Facilities, Visiting Staff Division and Foreign Visiting Staff Division. Among these, Synchrotron Radiation Laboratory has a branch in the High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki and the Neutron Science Laboratory maintains apparatus installed at the research reactor in the Japan Atomic Energy Agency, Tokai, Ibaraki. In addition, supporting facilities, which include Cryogenic Laboratory, Model Shop, Radiation Safety Laboratory, Library and International Liaison Office provide services to both in-house and outside users.

  New research positions as professors, associate professors and research associates of ISSP are advertised publicly. Candidates are selected by the Selection Committee consisting of nearly equal numbers of in-house and outside members and then approved by the Faculty Meeting. Some of the positions have own finite terms of appointment.