I have lived in Hokkaido for the past 3 years and though not flying in the GA scene, can tell you it exists. There are a couple of flying schools here is Sapporo (Okadama AP) but as has been pointed out, it is pretty pricey. Alpha (you were given a link) seems to be the only one with english capability and I know they have at least one english speaker there.
There is a glider park somewhere in central Hokkaido (Asahikawa maybe) also.
Need and info drop me a pm.