Japan Ministry of International Trade and Industry
Good publications list, such as White papers, Charts and Tables Related to Foreign Direct Investment in Japan, Fact Sheets Regarding Recent Trade Developments of the U.S. and Japan, Survey on Impact of Exchange Fluctuations, Statistics on Japanese Industries 1997, Industrial Statistics Monthly, Journal of Japanese Trade and Industry, etc. Good statistical section.
Japan Ministry of Transport
Highlights transportation services, etc., regionally throughout Japan.
Japan Statistics Bureau
Good source of summary statistics and links to all Japanese statistical agencies.
JETRO, Japan External Trade Association
The best internet sources for Japan reviewed here. An excellent collection of services offered, Japanese statistics, publications, links to other sites, etc. Also a Vancouver branch at http://www.canadex.com/jetrovan/
Library of Congress Japan Study
A very comprehensive study of Japan, including a country profile, history, society, economy, trade, politics, international relations, etc, plus a search engine. Link back to the Library of Congress' main page for similar studies on an impressive number of countries.