Before the WWII, documents were collected under the accountability toward the Emperor, not for the people of Japan. After the WWII, many of the administrative documents were discarded, because they didn't have the concept that the administrative documents were public property, but more "private" because the administrators produced them. Some of those documents were sold for the old book dealers, and therefore, sometimes, those public documents are found in old book market.
Some documents were taken by the United States and used for the International Military Tribunal for the Far East in Tokyo. Therefore they are no longer "top secret" documents. However, many Japanese scholars do not realize this point and go to the National Archives of the United States.
Japan Center for Asian Historical Records offers "a full-fledged digital archives, under Japan National Archives". It provides "Japanese modern historical records of relationship with various neighboring countries and regions, access through the Internet." (from their homepage http://www.jacar.go.jp/asia_en/index_en.html)
It took them 4 years to set up this center, but by the time when the center started its function, a new technology of minimizing file size became available. It enable the center to serve their documents to public in better condition.
Mr. Muta gave us hands-on exercise of using their database. It was very useful.