Japanese Government Agencies 

Defense Agency (under the Cabinet Office)
http://www.mod.go.jp/e/index.html

Ministry of Agriculture, Forestry, and Fisheries of Japan (MAFF)
http://www.maff.go.jp/e/index.html

Ministry of Education, Culture, Sports, Science and Technology (MEXT)
http://www.mext.go.jp/english/

Ministry of Environment (ENV)
http://www.env.go.jp/en/

Ministry of Health Labor and Welfare (MHLW)
http://www.mhlw.go.jp/english/index.html

Ministry of International Affairs and Communications (MIC)
http://www.soumu.go.jp/english/icpb/index.html

Ministry of Land, Infrastructure and Transport (MLIT)
http://www.mlit.go.jp/en/index.html

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National Institutes and Agencies in Japan

Geological Survey Institute (GSI)
http://www.gsi.go.jp/ENGLISH/

Institute for Molecular Sciences (IMS)
http://www.ims.ac.jp/

National Institute for Basic Biology (NIBB)
http://www.nibb.ac.jp/en/about/outline.html

National Institute for Fusion Science (NIFS)
http://www.nifs.ac.jp/

National Astronomical Observatory of Japan (NAOJ)
http://www.nao.ac.jp/E/

National Institute for Physiological Sciences (NIPS)
http://www.nips.ac.jp/eng/

Japan Aerospace Exploration Agency (JAXA)
http://www.jaxa.jp/index_e.html

Japan Atomic Energy Agency (JAEA)
http://www.jaea.go.jp/english/index.shtml

Japan Science and Technology Agency (JST)
http://www.jst.go.jp/EN/

National Institute of Natural Sciences (NINS)
http://www.nins.jp/english/

National Institute of Advanced Industrial Science and Technology (AIST)
http://www.aist.go.jp/index_en.html

National Agriculture and Food Research Organization (NARO)
http://www.naro.affrc.go.jp/index_en.html

National Institute of Environmental Studies (NIES)
http://www.nies.go.jp/gaiyo/index-e.html

National Institute of Genetics (NIG)
http://www.nig.ac.jp/english/index.html

National Institute of Health Sciences (NIHS)
http://www.nihs.go.jp/english/index.html

National Institute of Informatics (NII)
http://www.nii.ac.jp/en/

National Institute of Information and Communications Technology (NICT)
http://www.nict.go.jp/about/index-e.html

National Institute of Materials Science (NIMS)
http://www.nims.go.jp/eng/

National Institute of Polar Research (NIPR)
http://www.nipr.ac.jp/english/

National Institute of Radiological Sciences (NIRS)
http://www.nirs.go.jp/ENG/index.html

National Institute of Resource and Environment (NIRE)
http://www.aist.go.jp/NIRE/index-e.htm

National Museum of Nature and Science
http://www.kahaku.go.jp/english/

National Research Institutes for Earth Science and Disaster Prevention (NIED)
http://www.bosai.go.jp/e/

RIKEN
http://www.riken.jp/engn/

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Japanese Universities

Major Universities:

Hokkaido University
http://www.hokudai.ac.jp/en/
http://www.hokudai.ac.jp/en/research/research_projects.html (Research)

Keio University
http://www.keio.ac.jp/index-en.html
http://www.keio.ac.jp/en/academics/faculties.html

Kyoto University
http://www.kyoto-u.ac.jp/en
http://www.kyoto-u.ac.jp/en/research (Research)

Kyushu University
http://www.kyushu-u.ac.jp/english/
http://www.kyushu-u.ac.jp/english/research/index.php (Research)

Ochanomizu University
http://www.ocha.ac.jp/en/index.html
http://www.sci.ocha.ac.jp/en/index_en.html (Faculty of Science)
http://www.hles.ocha.ac.jp/e/index.html (Faculty of Human Life and Environmental Science)

Osaka University
http://www.osaka-u.ac.jp/en/
http://www.es.osaka-u.ac.jp/en/index.html (Graduate School of Enginnering)
http://www.eng.osaka-u.ac.jp/en/index.html (Graduate School of Engineering Science)
http://www.fbs.osaka-u.ac.jp/index-e.php (Graduate School of Frontier Bioscineces)
http://www.sci.osaka-u.ac.jp/index.html (Graduate School of Scinece)

Tohoku University
http://www.tohoku.ac.jp/english/
http://www.tohoku.ac.jp/english/researcher/ (Research and Cooperation with Industry)

Tokyo Institute of Technology
http://www.titech.ac.jp/english/

Tokyo University
http://www.u-tokyo.ac.jp/en/

Graduate Schools

School of Engineering
http://www.t.u-tokyo.ac.jp/etpage/

Graduate School of Agriculture and Life Sciences
http://www.a.u-tokyo.ac.jp/english/index.html

Graduate School of Medicine and Faculty of Medicine
http://www.m.u-tokyo.ac.jp/english

Graduate School of Science
http://www.s.u-tokyo.ac.jp/en/

Research Institutes

Center for Climate System Research
http://www.ccsr.u-tokyo.ac.jp/ehtml/eccsr.shtml

Earthquake Research Institute
http://www.eri.u-tokyo.ac.jp/index.html

Environmental Science Center
http://www.esc.u-tokyo.ac.jp/english/index-e.html

Information Technology Center
http://www.itc.u-tokyo.ac.jp/index-e.html

Institute of Cosmic Ray Research
http://www.icrr.u-tokyo.ac.jp/index_e.html

Institute of Industrial Science
http://www.iis.u-tokyo.ac.jp/index_e.html

Institute of Molecular and Cellular Bioscience
http://www.iam.u-tokyo.ac.jp/index.html

Institute for Solid State Physics
http://www.issp.u-tokyo.ac.jp/index_en.html

International Center for Elementary Particle Physics
http://www.icepp.s.u-tokyo.ac.jp/index-e.html

Molecular Genetics Research Laboratory
http://park.itc.u-tokyo.ac.jp/mgrl/index_E.html

New: Atomosphire and Ocean Research Institute
http://www.aori.u-tokyo.ac.jp/english/index.html

Research Center for Advanced Science and Technology (RCAST)
http://www.rcast.u-tokyo.ac.jp/en/

VLSI (Very Large Scale Integration) technology Design and Education Center
http://www.vdec.u-tokyo.ac.jp/English/index.html

Tsukuba University
http://www.tsukuba.ac.jp/english/
http://www.tsukuba.ac.jp/english/organization/

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Funding Sources for Scientific Research in Japan

Japan Foundation
http://www.jpf.go.jp/e/index.html

Japan Science and Technology Agency, Stratgic Basic Research Programs
http://www.jst.go.jp/kisoken/en/

Japan Society for Promotion of Science
http://www.jsps.go.jp/english/index.html

Sasakawa Peace Foundation
http://www.spf.org/e/

Social Science Research Council (SSRC)
http://www.ssrc.org/fellowships/

Compiled by Tomoko Y. Steen, Updated May 2012