Ministry of Foreign Affairs collects, classifies, and preserves Japan’s diplomatic records including valuable treaties and other historical documents from the end of the Tokugawa period to the present day. (In Japanese)
アジア歴史資料センター ・国立公文書館 The center aims to provide Internet access to Asia-related official documents held by three national archival collections. 225,000 catalog records and 2.7 million images are available so far.
国立公文書館 Searchable catalog of 490,000 volumes of Naikaku bunko, which includes official documents since the Edo government and other historically significant books and manuscripts.
幕末明治期日本古写真画像データベース・長崎大学 Searchable archive of 5,414 photographs of Nagasaki and other parts of Japan taken during the latter half of the 19th century (1860 -1920) . An English / Japanese site.
日本空襲デジタルアーカイブ a bilingual digital archive dedicated to the international dissemination of information about the United States Army Air Force air raids against Japan.
"Commissioned by the CIA, carried out by the Harvard program for the Study of Intelligence and Policy, examining the final months of WW2, including plans for invasion and the use of the atomic bomb."
"Nagasaki Journey features the archive of Yosuke Yamahata, a Japanese army photographer who documented the immediate aftermath of the atomic explosion at Nagasaki."