Getting basic stats on Japan's HE system

These sources are easily accessed and downloaded in standard formats. However, they are only up to 2006. To get up to 2008, you have to go looking for the information in various online publications. Here is a sample of what you can get. 

http://www.mext.go.jp/english/statist/index.htm
http://www.mext.go.jp/english/statist/index11.htm

University and Junior College

Universities          
Junior Colleges    
Students by Course (University)    
Students by Course (Junior College)    
Students by Field of Study (University)    
Students by Field of Study (Junior College)    
Students by Field of Study (Master's Courses)    
Students by Field of Study (Doctor's Courses)    
Students by Field of Study (Professional Degree Courses)    
Students of Non-Japanese Nationality    
Students from Abroad by Region of Origin    
Students from Abroad by Field of Study    
Full-time Teachers by Type of Position (University)    
Full-time Teachers by Type of Position (Junior College)    
Full-time Non-teaching Staff by Type of Position    
Correspondence Courses    
New Entrants (University)    
New Entrants (Junior College)    
New Entrants (Master's Courses)    
New Entrants (Doctor's Courses)    
New Entrants (Professional Degree Courses)    
First Destination of New Graduates (University)    
First Destination of New Graduates (Junior College)    
First Destination of New Graduates (Master's Courses)    
First Destination of New Graduates (Doctor's Courses)/(Professional Degree Courses)    
New Graduates Entering Employment (University)    
New Graduates Entering Employment (Junior College)    
New Graduates Entering Employment (Master's Courses)    
New Graduates Entering Employment (Doctor's Courses)/(Professional Degree Courses)    

Some new links for English-language info. on Japan HE

These are some links to Ministry of Education web pages which contain information and statistics on higher education here. At least the statistics look to be updated frequently.

http://www.mext.go.jp/english/koutou/index.htm

http://www.mext.go.jp/english/statist/index10.htm

http://www.mext.go.jp/english/statist/index11.htm