All Visa related activities are administered by the Ministry of Foreign Affairs (MOFA). There are several visa offices located in all parts of the country as well as Embassies and Foreign Consulates worldwide. The type of visa varies according to the nature of stay and duration. All foreigners are advised to contact the nearest relevant office and the official website for more information.

Links:
http://www.mofa.go.jp/j_info/visit/visa/
http://japan.visahq.com/
http://www.jnto.go.jp/eng/arrange/essential/visa.html