- 2022/11 - Person who has made outstanding cultural contributions
- 2018/12 - Cabinet Secretariat, Office of Healthcare Policy The Japan Medical Research and Development Grand Prize, the Healthcare Policy Minister's Prize Basic studies on molecular target drug discovery based on epigenetic regulation
- 2018/04 - 公益財団法人 長瀬科学技術振興財団 長瀬研究振興賞 新規抗真菌抗生物質 ASP2397 の作用機序に関する化学遺伝学的研究
- 2017/02 - Princess Takamatsu Cancer Research Fund Princess Takamatsu Cancer Research Fund Prizes Chemical biology on cancer therapy targeting regulatory molecules of epigenetics
- 2015/06 - The Japan Academy Japan Academy Prize Studies on Regulation of Eukaryotic Gene Expression using Bioactive Microbial Metabolites and their Application to Drug Discovery
- 2013/06 - The Japanese Association for Molecular Target Therapy of Cancer Tsuruo Takashi Award
- 2012/11 - Johns Hopkins University Lectureship Award, Charles E. Dohme Memorial Lecture 2012 Opening new frontiers through chemical genetics of natural products
- 2012/03 - RIKEN Significant Achievement Award for Achievement Worthy of Distinguished Award
- 2011/05 - Japan Society for Bioscience, Biotechnology, and Agrochemistry Japan Society for Bioscience, Biotechnology, and Agrochemistry Award
- 2010/04 - Minister of Education, Culture, Sports, Science and Technology Prizes for Science and Technology
- 2009/10 - Japan Bioindustry Association Japan Bioindustry Association Award
- 1998/11 - Japan Antibiotics Research Association Sumiki-Umezawa Memorial Award
- 1991/03 - Japan Society for Bioscience, Biotechnology, and Agrochemistry Japan Society for Bioscience, Biotechnology, and Agrochemistry Award for the Encouragement of Young Scientists