There is a national Japanese User's group that I am aware of.
There is or was a local User's group in Osaka, and another in Kyoto. There are a number of independent users as well. I maintain the alife program Tierra where I work at a research facility (which lets me maintain the Amiga port).
Tierra Home PageA new release of Tierra is due in the next couple of days for Linux/Unix/Windows. The Amiga port will follow shortly after that. I'll keep you posted on that. There is still life Amiga-wise around these parts.