Basically, in one of their sillier decisions, the powers that be in Japan have decided that offering prepaid cell phone service to non-residents encourages international terrorism or drug dealing or something stupid like that. So while it isn't actually illegal to do so, all the operators have "voluntarily" stopped doing it. That's why your choices are either

(a) get a phone from your hotel (I know of two luxury hotels in Tokyo that include this with your room, sometimes only upon request)

(b) rent one over the internet before departing, for hotel pickup
(cheapest rental option, I hear)

(c) rent one at the airport

(d) get a resident you know to purchase a prepaid phone and loan/give it to you. Once you have it, you can buy top-ups with no further problem.

(e) use your international 3G phone in Japan, typically for ridiculously expensive charges per call.