| JPN-28 | National Institute of Infectious Diseases | Tokyo | JAPAN | WPRO | WHO Collaborating Centre for Standardization and Evaluation of Biologicals | DIORDITSA Sergey | Active | Details |
| JPN-31 | National Cancer Centre | Tokyo | JAPAN | WPRO | WHO Collaborating Centre for Reference on Smoking and Health | AUDERA-LOPEZ Maria Carmen | Pending | Details |
| JPN-32 | Radiation Effects Research Foundation (RERF) | Hiroshima | JAPAN | WPRO | WHO Collaborating Centre for Research on Radiation Effects on Humans | CARR Zhanat | Active | Details |
| JPN-34 | Juntendo University | Bunkyo-ku | JAPAN | WPRO | WHO Collaborating Centre for Prevention of Blindness | KOCUR Ivo | Active | Details |
| JPN-35 | Nagasaki University Graduate School of Biomedical Sciences | Nagasaki | JAPAN | WPRO | WHO Collaborating Centre for Research and Training in Mental Health | WANG Xiangdong | Pending | Details |
| JPN-38 | Research Institute of Tuberculosis (RIT) | Kiyose | JAPAN | WPRO | WHO Collaborating Centre for Reference, Research and Training on Tuberculosis | VAN WEEZENBEEK Catharina Simonne Beatrix | Active | Details |
| JPN-45 | National Centre for Global Health and Medicine (NCGM) | Tokyo | JAPAN | WPRO | WHO Collaborating Centre for Health Systems Research | POSTMA Sjieuwke Eelco Jozef | Active | Details |
| JPN-46 | Kitasato University | Tokyo | JAPAN | WPRO | WHO Collaborating Centre for Traditional Medicine | SAMDAN Narantuya | Active | Details |
| JPN-49 | National Institute for Minamata Disease | Minamata | JAPAN | WPRO | WHO Collaborating Centre for Studies on the Health Effects of Mercury Compounds | HASSAN Mohd Nasir | Active | Details |
| JPN-50 | National Institute of Public Health (NIPH) | Saitama | JAPAN | WPRO | WHO Collaborating Centre for Healthcare Facility Planning and Service Delivery | POSTMA Sjieuwke Eelco Jozef | Active | Details |