But if you wan't to extend your stay you must go to the immigration office in Japan or try to call to the ambassade of your country in Japan and ask them how to extand your stay, they proly give you the number for the immigration office.

Also, it is not true that "praticly all country you can stay in Japan 90 days without visa". Only the citizens of about a third of the world's countries can do so. Details are below:
http://www.mofa.go.jp/j_info/visit/visa/02.html

One or two days may be possible- one or two months almost definitely not.

*Other visas may or may not be extended, depending on your nationality, whether the activity for which the visa was issued is completed, and so on. In some cases, you may be granted a tourist visa for a few days to a couple of weeks in order to extend your activities in Japan, but this will again be at the discretion of the Immigration Office. If you can provide sufficient reason, then your chances of being awarded an extension are of course greater.
www.mofa.go.jp/j_info/visit/visa/01.html -