The JAPAN NGO DIRECTORY 
This directory provides a starting point for those wishing to contact some of the more active NGOs in Japan. The directory is divided into categories. 
NPO Hiroba
Provides statistics about the number and field of activity of NPOs in Japan. Can be searched by year, type, region. Lists 36,869 current NPOs. 
JANIC (Japan NGO Center for International Cooperation) 
Includes a directory of 289 NGOs involved in international cooperation.
Japan NPO Center
Links to many relevant internet sites organized by focus (international cooperation, corporate philanthropy, art, gender equality, environment, welfare and citizen activities, social education, community design, labor, consumer problems.) Also links to NPO Hiroba.  
Japan NPO Research Association  
Japan Web links for NGOs and Volunteer groups 
NPO Homepage, sponsored by the Cabinet

The Japan Policy Research Institute
JPRI was founded in 1994 as a non-profit membership organization and headed by Chalmers Johnson, seeks to promote understanding of Japan's political economic behavior and growing significance in world affairs. It has just released its rather large corpus of papers published in 1996. The site is a serious tour de force of Japan scholars and a must-have resource for students and teachers alike. 
Asia Policy Point's blog
The Point is the blog of Asia Policy Point, an independent Washington, DC, research center studying US-Asia policy. It identifies and discusses research tools for the Asia policy analyst.