I used to work in this area, Tsukuba Science City, though I was not involved with the nuclear reprocessing itself, so don't blame me for that whole plutonium thing.
What it does is gather spent nuclear fuel from Japan's many commercial reactors, breaking it down into "unburned" uranium, which goes back into new fuel rods, plutonium, which because of its military potential is burned in specially optimized reactors of its own, and miscellaneous isotopes. The fraction of the miscellaneous isotopes that can't be used for anything is stored - a far smaller volume than we're talkking about doing in Nevada. This facility can also recycle fuel from many foreign sources.
Yeah, sure, they ALWAYS say that! :o)