วัฒนธรรมและสังคมศึกษา School of Cultural and Social Studies

• Department of Regional Studies, National Institutes for the Humanities, National Museum of Ethnology
• Department of Comparative Studies, National Institutes for the Humanities, National Museum of Ethnology
• Department of Japanese Studies, National Institutes for the Humanities International Research Center for Japanese Studies
• Department of Japanese History, National Institutes for the Humanities, National Museum of Japanese History
• Department of Cyber Society and Culture (Termination of student recruitment), The Open University of Japan Center for Open Distance Education
• Department of Japanese Literature, National Institutes for the Humanities, National Institute of Japanese Literature

วิทยาศาสตร์กายภาพ School of Physical Sciences

• Department of Structural Molecular Science, National Institutes of Natural Sciences a Institute for Molecular Science
• Department of Functional Molecular Science, National Institutes of Natural Sciences a Institute for Molecular Science
• Department of Astronomical Science, National Institutes of Natural Sciences, National Astronomical Observatory
• Department of Fusion Science, National Institutes of Natural Sciences, National Institute for Fusion Science
• Department of Space and Astronautical Science, Japan Aerospace Exploration Agency, Institute of Space and Astronautical Science

วิทยาศาสตร์เครื่องเร่งอนุภาคพลังงานสูง School of High Energy Accelerator Science

• Department of Accelerator Science, High Energy Accelerator Research Organization (Tsukuba Campus) Accelerator Laboratory・Applied Research Laboratory
• Department of Materials Structure Science, Institute of Materials Structure Science
• Department of Particle and Nuclear Physics, Institute of Particle and Nuclear Studies

สหวิทยาศาสตร์ School of Multidisciplinary Sciences

• Department of Statistical Science, The Institute of Statistical Mathematics
• Department of Polar Science, National Institute of Polar Research
• Department of Informatics, National Institute of Informatics

วิทยาศาสตร์ธรรมชาติ School of Life Science

• Department of Genetics, National Institute of Genetics
• Department of Basic Biology, National Institute for Basic Biology
• Department of Physiological Sciences, National Institute for Physiological Sciences

วิทยาศาสตร์เพื่อนวัตกรรม School of Advanced Sciences

• Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies [Hayama campus]