Location
Major Ida Masataka of the Ministry of War of Japan and later of Kyujo Incident fame, proposed the location. After the general staff approved of it, the Railway Ministry conducted a survey of the area, finalising the plans to build such a complex. Five points were raised in Ida's proposition;
1) the widest flat area in Honshu, with an airstrip nearby;
2) solid substrate suitable for excavation and ability to withstand 10 ton bombs;
3) completely surrounded by mountains, yet having sufficient flat surface area for underground constructions;
4) abundance of labour (later proven untrue);
5) Nagano prefecture's residents are simple, making the concealment of the facility easier; the old name for Nagano, Shinshu rhymed with God's Land, and is auspicious.
This proposition primarily involved setting up bunkers for the army throughout the Japanese homeland. It was afterwards, that Prime Minister Tojo Hideki expanded the project to accommodate the transfer of the government.
While the project was an operational secret in the guise of a warehouse, from the statement of a local Japanese labourer, rumours were rife in the surrounding villages and towns that the emperor was coming to town. The cause of the rumours was due to the massive amounts of cargo that came on trains.
Read more about this topic: Matsushiro Underground Imperial Headquarters