The Immigration Bureau controls all matters regarding entry and residency for foreigners in Japan. Its website contains information on immigration matters, procedures, sample forms and contact information for immigration centers throughout Japan.
It should be noted that the immigration system has undergone many changes especially in the area of Residence Management. The changes went into full effect beginning July 9, 2012. All the changes are explained in a special section of the Immigration Bureau of Japan website.
For further information on the new immigration system, please refer to here
Tokyo Regional Immigration Bureau
5-5-30 Konan, Minato-ku, Tokyo
Yokohama District Immigration Office
10-7 Torihama-cho, Kanazawa-ku, Yokohama-shi, Kanagawa