Sorry, Japanese DEM data is not free now.  Geographical Institute Survey publishes DEM and  restricts  its usage.
You can purchase DEM from GIS but I feel it's bit pricey.
http://www.gsi.go.jp/ENGLISH/MAPS/map-geo.html

I recommend to try   Japanese EF's tutorial.
http://content.e-frontier.co.jp/e-on/efimage/srtm_dem.html
Written in Japanese and for Vue5, but maybe you can translate it.
The page says:
1.Get SRTM from NASA site. Japanese data is in Eurasia folder and Fuji mt. data is in N35E138.hgt.zip.

2. Get 3DEM and convert SRTM into DEM.
3. Revise the data in 3DEM and export DEM data.

Hope this helps:-)

Hatsumi