My friends in Yamanashi play on weekends. They get their stuff from Yellow Submarine in Tokyo. I think there are some groups that meet up either at the Yellow Sub stores, or can tell you who to talk to. You could also try some of the Japanese table top games.
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They meet in Tokyo, and have groups in other areas (I know the people in Kanagawa but rarely have time to meet and play anything).
They are very nice people and play a wide variety of games.
Here's a link:
http://jigg-japan.blogspot.com/
There's a yahoo group which people use to arrange stuff - there's a link on that page.
I really do recommend them - they're very welcoming and someone's playing something just about every weekend (or even weekday).