Here is a current list of the top 5 universities in Japan.

Update: I have received some e-mails asking me if these Universities offer courses and degrees in English. I have updated each one with links to the University websites showing full details. You can also download this PDF list of universities and the degrees offered in English that I got directly from http://www.jasso.go.jp/index_e.html Here’s another site you might find useful if you’re looking for courses taught in English – http://www.jpss.jp/en/univ/english/

1. The University of Tokyo – (Tokyo Daigaku) a major research university. Fifteen prime ministers in Japan have studied at University of Tokyo. During the Summer Olympics in 1964, the university hosted the running portion of the pentathlon event. The University’s School of Science and the Earthquake Research Institute are both represented on the national Coordinating Committee for Earthquake Prediction. Here’s a list of Degrees Offered in English.
   
2. Kyoto University – (Kyoto Daigaku) It is the second oldest Japanese university, and formerly one of Japan’s Imperial Universities. The university claims six Nobel Laureates and two Fields Medalists among its faculty and alumni. Here are Degree Programs in English for International Students.
   
3. Osaka University – (Osaka Daigaku) It is the sixth oldest university in Japan, and formerly one of Japan’s Imperial Universities. Not only is it one of the top research institutions in Japan, it’s very difficult to get into. They offer English Degrees and Courses taught in English.
   
4. Nagoya University – (Nagoya Daigaku) It is one of the most prestigious universities and it’s one of the top research institutions in Japan, and Nagoya Law School is considered as one of top Law schools in the country. It’s very selective with the students they select. They offer undergraduate degrees from which students can graduate entirely in English.
   
5. Tohoku University – (Tohoku Daigaku) It is the third oldest Imperial University in Japan and one of the 13 universities selected by the government to lead the internationalisation of higher education in Japan. They offer international degree courses taught completely in English, at both undergraduate and graduate level. The radiology department has been actively measuring radiation levels throughout the city of Sendai since the Fukushima Nuclear Power plant meltdown, which is about 100 kilometers south. One of the interesting research centers they have is the Research Center for Prediction of Earthquakes and Volcanic Eruptions. They also offer International degree programs taught in English.
   You can view the top Japanese Universities and see where they stand in the country of Japan as well as where they are listed in top 500 worldwide rankings right here.