If price is the number one factor, then you might consider

(1) Rent (or get a friend to buy) a local phone
Then use a calling card for the international calls - prepaid from a convenience store in Japan. Or have your office call you back on that local number.
If you're using a calling card, you may find that the call quality is better from a fixed line phone than from a mobile. (And the card lasts longer).

(2) Use Skype
If you subscribe to a service like iPass, you can use wireless hotspots in many fast food joints and cafes around Tokyo (including Dotour, McDonalds etc. - but not Starbucks). Hook up your PC, dial up the office and annoy the hell out of your neighbours in the cafe. (And hope that your colleagues don't mind the background noise: "Do you want fries with that?")

(3) Two yoghurt cups and a long length of twine