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You may want to visit Yahoo Auctions, or Yahoo Shops Japan. I think they use a combination of bank, postal transfers, and also Sony's e-bank. They also have their own system called Yahoo Wallet, which integrates into your ISP broadband service, credit card / or bank payments.
I have sent several detailed emails to Paypal about their Japanese language situation and they don't seem very interested.
We spent US$550 to sign up with WorldPay for their system, but their compliance requirements and whole approval system was a nightmare. In the end we did our money on this.
At the moment we are back to appling for a merchant facility with a bank in Australia. The biggest problem is the customers don't sign the voucher in front of us so the banks don't like it.
I am sure there is an option out there, but the question is at what price. It also depends on the type of product you are selling and how. We have several requirements and the are not just for the Japanese market.
Yahoo Auctions, or Yahoo Shops Japan
Yahoo Japan is the most well known web property in Japan. Their portal is also the top ranked in terms of traffic. Their Auctions and Shops would certainly lend credibility in terms of name recognition. Although this is not a PayPal type solution maybe your service could make use of these systems.
Just for your reference I posted some Japanese traffic figures in this thread: Google 10th most popular SE in Japan [webmasterworld.com]
You can see the lead Yahoo Japan has on the other sites.