Yeah, they became illegal in 2003 or 2004 or something, but before then you could go and buy a big bag of shrooms in the many headshops of Osaka and I'm sure Tokyo too.
An interesting thing is that mescaline is illegal, but it is legal to sell and grow cactii such as peyote and san pedro, but its illegal to grow them for the mescaline inside of them. Though this is Japan, so it probably costs an arm and a leg.
Of course drugs are evil becuase they make you put guns in your mouth while you giggle like a schoolgirl. Unless of course, its sold by large corporations (id est nicotine), in which case, you'll end up as a cool looking american cowboy.