When I moved from Japan to Switzerland years ago, I used the services of Japan Luggage Express http://www.jluggage.com
to send my personal items. It is a company in Japan but when I returned to Japan a few years later I contacted them again to ask if they offer service from Switerland to Japan and they were able to arrange it. Their agent collected about 10 boxes from my residence in Zurich and I sent them by air. It was quite a smooth move. I have moved internatioally a couple of times in the past and if you are shipping to Japan and your shipment is not very large it is better by air because charges you need to pay after the boxes arrive at the other end can be very expensive if you ship by boat. I do not know how many boxes or kilograms you are shipping but I imagine that you are not shipping something like furniture, so I recommned that you get a quote from this shipping company. Their charges are quite reasonable and they provide very good communication, so I would highly recommend them. Also, you can ship by airfreight through some international moving company and then ask a company like JLE to custom clear once the shipment arrives in Japan. Once again, sea shipping could be expensive for small shipments and also whereas post office is good if you are sending only a few packages, if you are shipping more than several of them it is better to use some freight company in Switerland or the Japanese company I recommnded.