A friend of mine just got accepted into a univeristy in Osaka (Kansai Gaidai for the record). He says all up he had:
-Japanese University 4 page main application
-Japanese University 6 page housing application
-3 letters of recommendation (can't be from Japanese teacher)
-Japanese proficiency 1 page
-Japanese teacher letter of recommendation/proficiency evaluation
-Medical information form (doctor visit!) 2 pages
-10 ID photographs (strange foreign size requirements, had to look all over for a place that could do it...)
-Personal Statement 1 page
He also had to fill out a foreign studies application which was 4 pages long from his university (since he is technically transferring there), not sure what you'd do in place of this though.
Umm that's probably not too much help, but that should give you an idea for what to expect and look for. I'd guess a place to start would be checking out their university websites (such as
http://www.kansaigaidai.ac.jp/ ) or even talking to your careers advisor at school.