Modern Maps
国土地理院 The Geospatial Information Authority of Japan (GSI)
Topographic Map of Japan, 1/25,000 scale ウォッちず 国土地理院地図閲覧サービス
Offered by the Geographical Survey Institute; Map of Japan in 1/25,000 scale is viewable.
JapanMap View Japan with many layers of information, including nuclear power plants, the railway network, local fire stations, etc. Originally created by Lex Berman after the 2011 triple disaster.
東京関係地図目録 Catalogs of Tokyo/Edo maps.
東京都公立図書館住宅地図総合目録 Union catalog of Tokyo residential maps from the Tokyo Public Library.
Historical Maps 歴史地図
Japanese Historical Maps, UC Berkely
Japanese Maps of Tokugawa Era University of British Columbia's 275 maps are viewable.
Historical Maps of Asia, Perry-Castañeda Library Map Collection, University of Texas at Austin
国会図書館絵図検索 535 historical maps are searchable, some with images.
Complete Survey of the Japanese Coast 大日本沿海輿地全図
The first geographical survey maps of Japan, made by Tadataka Ino, and often known as the Ino maps 伊能図. This site provides digital images of 43 sheets, as well as options to view the entire map (some sheets have been lost) and to zoom in. There is also a comprehensive geographical name index including old, modern, and natural place names. Created by the National Diet Library.
Dai Nihon enkai yochi zenzu 大日本沿海輿地全図 / / Inō daizu / [Inō taizu] / [Japan, Hokkaido to Kyushu] This nearly-complete set of 207 sheets was discovered at the Library of Congress in 2001.
徳島大学古地図コレクション Tokushima Daigaku Map collection
国立公文書館絵図（江戸時代） Edo period maps and images from the National Archive of Japan.
乾隆京城全図 Complete Map of Peking, Qianlong Period 東洋文庫蔵
Harvard Map Collection: Japan related Enter "Japan" in the search field. Includes 81 viewable images.
Search & Tools
Harvard Map Collection Shelflist
WorldMap Open source map-creation tool.
GIS
Historical Data by region 歴史地域統計データ Created and maintained by Tsukuba University.
Harvard Geospacial Library Download geographic data for use with GIS software.
Japan Dataverse from Skinner Regional Systems Analysis
Gaihozu 外邦図
Gaihōzu: Japanese Imperial Maps
外邦図研究プロジェクト led by Prof. Shigeru Kobayashi, Osaka University. 『外邦図研究ニューズレター 』is available in pdf.
アメリカ議会図書館蔵初期外邦測量原図データベース Early Japanese Military Maps of Korea and China held by LC
Gaihōzu: Japanese Imperial Maps 120 sets of maps held by the Stanford University are viewable.
Secret Japanese Military Maps Could Open a New Window on Asia's Past by Greg Miller in National Geographic (Aug. 2016)