The Japan Immigration Procedures Guidebook
The link below has simple flowcharts, explanations and Q&A to provide guidance on a variety of Japan immigration control procedures. The information contained in this link includes:
1. Immigration control procedures for foreign nationals
2. Residence procedures for foreign nationals
3. Deportation and Departure Order system
4. Recognition of refugee status
5. Alien registration
6. Application written example
7. Application forms in Adobe PDF format (printable on an A4 sized bond paper)
http://www.immi-moj.go.jp/english/tetuduki/t_main.html#zairyuu