Kyoto University (source)

As of 2010, there were 86 national universities (国立大学 kokuritsu daigaku?), 95 public universities and 597 private universities in Japan.[1] National universities tend to be held in higher regard in higher education in Japan than private or public universities.
 
In 2004, the national university system underwent partial privatization. Since 2004, every national university has been incorporated as a "national university corporation" (国立大学法人 kokuritsu daigaku hōjin?) and given considerable autonomy in its operations. Faculty and staff are no longer government employees (国家公務員 kokka kōmuin?) working for the Ministry of Education, Culture, Sports, Science and Technology. University names which shifted are "graduate university" (大学院大学 daigakuin daigaku?).
 
The following is a complete list of Japanese national universities:
 

• Aichi University of Education
  Akita University
  Asahikawa Medical University
  Chiba University
  Ehime University
  Fukuoka University of Education
  Fukushima University
  Gifu University
  The Graduate University for Advanced Studies
  Gunma University
  Hamamatsu University School of Medicine
  Hirosaki University
  Hiroshima University
  Hitotsubashi University (former Tokyo College of Commerce)
  Hokkaido University (former Hokkaido Imperial University)
  Hokkaido University of Education
  Hyogo University of Teacher Education
  Ibaraki University
  Iwate University
  Japan Advanced Institute of Science And Technology
  Joetsu University of Education
  Kagawa University
  Kagoshima University
  Kanazawa University
  Kitami Institute of Technology
  Kobe University
  Kochi University
  Kumamoto University
  Kyoto Institute of Technology
  Kyoto University (former Kyoto Imperial University)
  Kyoto University of Education
  Kyushu Institute of Technology
  Kyushu University (former Kyushu Imperial University)
  Mie University
  Miyagi University of Education
  Muroran Institute of Technology
  Nagaoka University of Technology
  Nagasaki University
  Nagoya Institute of Technology
  Nagoya University (former Nagoya Imperial University)
  Nara Institute of Science and Technology
  Nara University of Education
  Nara Women's University
  Naruto University of Education
  National Graduate Institute for Policy Studies
  National Institute of Fitness and Sports in Kanoya
  Niigata University
  Obihiro University of Agriculture and Veterinary Medicine
  Ochanomizu University
  Oita University
  Okayama University
  Osaka Kyoiku University
  Osaka University (former Osaka Imperial University)
  Otaru University of Commerce
  Saga University
  Saitama University
  Shiga University
  Shiga University of Medical Science
  Shimane University
  Shinshu University
  Shizuoka University
  Tohoku University (former Tohoku Imperial University)
  Tokyo Gakugei University
  Tokyo Institute of Technology
  Tokyo Medical and Dental University
  Tokyo University of Agriculture and Technology
  Tokyo University of Foreign Studies
  Tokyo University of Marine Science and Technology
  Tokyo University of the Arts
  Tottori University
  Toyohashi University of Technology
  Tsukuba University of Technology
  University of Electro-Communications
  University of Fukui
  University of Miyazaki
  University of the Ryukyus
  The University of Tokushima
  The University of Tokyo (former Tokyo Imperial University)
  University of Toyama
  University of Tsukuba
  University of Yamanashi
  Utsunomiya University
  Wakayama University
  Yamagata University
  Yamaguchi University
  Yokohama National University

Although The Open University of Japan and Okinawa Institute of Science and Technology are founded by the national government's initiatives and heavily subsidised by the government, they are classified as private.

(source : Wikipedia)