Inter-University Research Institute Corporation National Institutes for the Humanities
- International Research Center for Japanese Studies
- National Institute for Japanese Language and Linguistics
- National Institute of Japanese Literature
- National Museum of Ethnology
- National Museum of Japanese History
- Research Institute for Humanity and Nature
Inter-University Research Institute Corporation National Institutes of Natural Sciences
- Institute for Molecular Science
- National Astronomical Observatory of Japan
- National Institute for Basic Biology
- National Institute for Fusion Science
- National Institute for Physiological Sciences
Inter-University Research Institute Corporation High Energy Accelerator Research Organization
- Accelerator Laboratory
- Applied Research Laboratory
- Institute of Materials Structure Science
- Institute of Particle and Nuclear Studies
Inter-University Research Institute Corporation Research Organization of Information and Systems
（Scientific Research Institutes Division, Research Promotion Bureau）