Biodiversity Center of Japan
- Monitors and evaluates the natural environment and its present level of biodiversity, and to assemble and maintain a public library of objective information.
- http://www.biodic.go.jp/english/index-en.html

Association of International Research Initiatives for Environmental Studies
- Organizes efforts to predict global environmental problems before they happen, learn as much and as quickly as possible about them, and take appropriate countermeasures.
- http://www.airies.or.jp/index_E.html

National Institute for Minamata Disease
- Conducts medical research to improve medical treatment for victims of Minamata disease (methylmercury poisoning) in Kumamoto, one of Japan's worst chemical poisoning disasters.
- http://www.nimd.go.jp/english/

National Institute for Environmental Studies (NIES)
- Conducts environmental impact research in such fields as climate change, biodiversity, water and waste management, deforestation, and pollution.
- http://www.nies.go.jp/