There was definitely a user's group in Kyoto until recently. Almost all of the members moved away over time because of the economy. The founder was very into overclocking, and had one of the first classic Amigas (non-PPC) to exceed 50 MHz. He modified his A4000T to get to about 70MHz back in the mid 90's as I recall. This was no small feat as Amiga support in Japan was almost non-existent, and he had to engineer most of it himself.
If memory serves, there may have been a Amiga user group in Osaka as well back in late 1980s. I have not heard anything about it in years though.
There was one in Tokyo which was active until about 2005 or so, and had quite some interest in the AmigaOne. This latter group was fairly active internally, but did not communicate with the Amiga community outside Japan as far as I know. I believe it has since gone inactive, though I think the website may still be online.
