Hi. I live in Tokyo. I think there are a few others here who do too.

Here are a few things to keep in mind:

1) what sizes are you looking for? It is nearly impossible to find a frame larger than 58 in Japan and even that is pretty rare. I know this well because I ride at least a 62cm frame.

2) used bikes (and really anything used) isn't as cheap here as you might expect. Vintage bikes and parts seem to go for a lot more here than they do in other countries.

There are a few shops in Tokyo that cater to cyclo touring. Particularly Velo Craft in Kichijoji (new and used) and Blue Lug (new only). Blue Lug has several locations around Tokyo. Unfortunately any thing you buy at those stores will probably be prohibitively expensive.
There is also Cycly who have a number of locations and only sell used bikes / equipment. You might get lucky there but they tend to be over priced. Cycle Paradise is another chain of used bike shops, usually even more over priced than Cycly.
There are also a few shops that specialize is nice vintage stuff. Hasegawa is by far the best among these and definitely worth a visit, but you're not likely to find anything affordable.

If you happen to ride a 64 cm frame I would be happy to lend out my Nishiki Sport beater repainted in baby pink.