While there are significant differences in the statistics made available in the United States and Japan, most of the statistics provided by the Japanese government can be found on the internet.
Japanese Government Statistics Bureau portal
Includes census data from 1995 and 2000 census. Maps from 1955-1995.
Japanese Government Ministries have their own statistics; see, in particular, the websites for:
Statistical Material for Learning about Japan
An English-language guide to statistical information about Japan, this site created by the National Diet Library of Japan introduces major statistical materials on Japan written in English, or in both Japanese and English. This finding aid presents both printed publications and web-accessible information.