I don't know much about those services, but I could find some like you want.
http://www.mediaweb.biz/product_info.php?cPath=23&products_id=246&osCsid=0d73a14903abef232a42287cc529409e
http://www.inet.ad.jp/server/
http://www.chiroro.co.jp/rental/package.html
BTW, do you speak Japanese?
I wonder that why do you need the server in Japan.
やまさん: There are many Linux distributions so people can choose their favorite one, the one which suites best their interest, etc. Going with your way of thinking, we all could just have the ultimate one Linux, thank God we have many.
しまでんさん: Of course Japanese website can be hosted anywhere in the World, but I guess that if Japanese website is hosted in Africa, it will lag a little.
I chose http://www.willnet.ad.jp/ , VPS is working very good.