Online dating in Japan been historically a bit of a shady business. Most online dating in Japan occurs on what are called "de-ai-kei" websites that are usually restricted to mobile phones online. The system is different from western online dating. Instead of paying a monthly membership fee, users pay per email communication within the system.
As you can imagine, this type of system has lead to a large number of scam companies who setup fake female accounts and create fake communications with male users in order to increase the revenue per subscriber.
Recently mainstream dating companies such as match.com have entered in Japan, adding a more legitimate and safe environment for daters. But match.com in Japan is limited to Japanese language only, so its not very friendly for foreign men who can not read or write Japanese.
Japan has another large dating company, o-net which is owned by e-commerce conglomerate Rakuten. The site is geared more towards Japanese who are interested in marriage, but many Japanese men use the site for casual dating. Unfortunately this site is also only in Japan.
The best solution for men in Japan or visiting Japan who would like to meet Japanese girls has been friendship website worldfriends. The site is mainly billed as a friendship and language exchange site, but plenty of users, male and female use it for dating purposes. And its bi-lingual so there should be no problem getting around the site. It's also free.
Photo by: iMorpheus