Calling abroad from Japan can be very expensive. So its important to look around for a deal that suits you. KDDI and NTT are two of the major service providers in Japan and have various packages that offer discounted call rates.
Using skype is another way of making cheap international calls. You might also consider investing in a VOIP phone.
For more detailed information on communications in Japan I suggest you take a look at the Keeping in Touch in Japan page.