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.

Comprehensive:

Nihon Tōkei Nenkan = Japan Statistical Yearbook
日本統計年鑑
EAC: HA4621 .J373;
Latest in EA Ref.
The basic statistical source, provides information on land & climate, population, national accounts, currency and flow of funds, public finance, business activities, agriculture, forestry and fisheries, mining and manufacturing, construction, energy and water, information and communication/science and technology, transport, domestic trade and services, finance and insurance, labor and wages, prices and land values, housing and estate, family income and expenditures, social security, health and sanitation, education, culture, government employees and elections, justice and police, environment, disasters and accidents, comparative international statistics. Statistics from the most recent edition available in Excel and PDF formats at http://www.stat.go.jp/english/data/nenkan/index.htm

Nihon Choki Tōkei sōran = Historical Statistics of Japan
日本長期統計総覧
EA Ref: HC462.7 .N475 1987
A compilation of the Japan Statistical Yearbook and its prewar predecessor, Nihon Teikoku Tōkei nenkan; covers 1885 to 1985. Unlike the latter, it includes defense statistics. The web version extended its time-series (1868-2002) and enriched the coverage of statistics; contains 836 statistical tables in 31 fields at http://www.stat.go.jp/english/data/chouki/index.htm

Japanese Government Statistics Bureau portal
English: http://www.stat.go.jp/english/data/
Japanese: http://www.stat.go.jp/
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:
 http://www.meti.go.jp/english/index.html

• Ministry of Economy, Trade and Industry (METI) http://www.meti.go.jp/english/index.html
• Cabinet Office http://www.cao.go.jp/index-e.html
• Ministry of Finance http://www.mof.go.jp/siryou.htm
• Ministry of Health, Labour and Welfare http://www.mhlw.go.jp/english/index.html
• Ministry of Education http://www.mext.go.jp/english/statist/index.htm
• Bank of Japan http://www.boj.or.jp/en/theme/research/index.htm
• Japan External Trade Organization (JETRO) http://www.jetro.go.jp/

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Prefectural Statistics

Shichōson jōhō sōran
市町村情報総覧
EAC: JS7373.A6 S53; latest in EA Ref.
A two-volume set covering eastern and western Japan containing hard-to-find statistical data for villages, towns and cities.

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Specialized Statistical Resources

Chōki keizai tōkei = Estimates of Long-Term Economic Statistics of Japan Since 1868
長期経済統計。 推計と分析 13 vols.
EA Ref: HA1845 .E8 1965  
Compiled by a team of economists after WWII to address the need for economic statistics for the wartime era and to create a continuous index.

Shuyō keizai, kinʾyū dēta CD-ROM.
主要経済金融データ CD-ROM [computer file]
See also Bank of Japan website http://www.boj.or.jp/en/howstat/index.htm
EAC CD-ROM: C80

Shakai seikatsu tōkei shihyō= Statistical Indicators on Social Life
社会生活統計指標
EAC: HN721 .S535
Covers population, economics, finance, education, labor, family budgets, housing, social security, health care, safety, allocation of daily time.