If you're in Japan and need to move within the country, or ship any size of items, I highly recommend using Yamato Transport, also known as Kuroneko 黒猫 (which means black cat). In Japan, Kuroneko is ubiquitous- maybe that's why it's so affordable.
I have used this company both times I moved within Japan, and they're very efficient, and so cheap. I never shipped any furniture, but when I moved to Osaka I shipped four big pieces of luggage, and it costs under 2,000 yen (about 25$) per bag. Surprisingly it's the same cost from Osaka to Tokyo, despite the distance being much greater.
A friend of mine recently relocated to Osaka, and there is a fixed price to move several boxes and large pieces of furniture. They also provide an English service, which is useful. Kuroneko has shipping points located everywhere all over Japan, from small convenience store counters to bigger housewares where you can buy boxes and special bags to ship your futon. I was particularly excited about the futon bag.
The people who work at my local Kuroneko know my pretty well by now, I've visited a few times to get boxes and inquire about shipping dates (they ship the next day), I think they find me quite entertaining.