Although my field of comparative expertise lies in the other end of the spectrum, I would like to emphasize that it is indeed possible to rent apartments in urban Japan that are larger than, say, 250 square feet.
Take this apartment (seen above), for instance.
Size: 389.6m² (approx. 4,194 ft²) Built: March 1995 Rent: 2,350,000 yen (approx. $21,357.81)
Not only is it, um, huge, it's also a six-minute walk from Azabujūban Station and the address is in href="http://en.wikipedia.org/wiki/Roppongi">Roppongi, probably the so-called Roppongi Hills area, to be precise. I would list its facilities, but I'm pretty sure you get the picture. (Yes, you get your own bathroom, &c.)
The funny thing is that this apartment is listed on the same website as the one where I found the cheap apartments in the entry I linked to at the beginning. This must be a total bargain in Roppongi Hills! So if you're filthy rich penny pincher and you want to rent an apartment in Tokyo, you might want to check out the websites for the hoi polloi, just in case. Make sure to set the minimum rent accordingly.