I typically know where to look for this data in the United States, but I'm at a loss when looking for building footprint shapefiles abroad. I thought I could find what I was looking for with Open Street Map data, but when I check out http://downloads.cloudmade.com/asia/eastern_asia/japan/tokyo#downloads_breadcrumbs I don't get the files I need. Anyone know other resources, either official or osm?
You can can try downloading the Japan OpenStreetMap data at Geofabrik. You can choose between pbf, bz2 or zipped shapefiles. It should have the files you need.
Good luck :)