Sorry for bumping up an old thread, but I thought I'd post an update so that no one ends up getting an old information should they stumble upon this thread. As this is money related thing, it seemed all the more important to me.
The limit was reduced by half to 50,000 yen for one withdrawal last summer, but recently I've found out it has been since restored to the original 100,000 yen limit again, which also applies to most Japanese ATMs in general as far as I know.