I hope this thread is appropriate! I help run a small B&B out here on my south European island and we just hosted our first Japanese guests. I've also been reading that Japanese tourists are showing an increased interest in rural tourism, which is fantastic because we're nothing but rural out here. We serve older Japanese daytourers in our restaurant on a bi-weekly basis but our accommodations see little Japanese interest/traffic on the host sites like TripAdvisor and Booking.com. Do Japanese travelers seek alternative travel reference sites? As I start to get the hang Japanese I'd very much like to increase my exposure.
Japanese like to have their hand held while on holiday because most of them can't speak English or any other language. So they tend to go with companies such as JTB since they have Japanese speaking staff on site at the location city in most cases. They also like to use a massive travel agent called H.I.S.
They would most likely book their trip through an agency such as JTB just as Yakumo said. I don't know how these sites work in terms of search results and ranking but are your listings at least in (native or professionally translated) Japanese? Rakuten Travel is also quite a large site.
Ideally, you need to offer a tour if you want Japanese business. You can spot Japanese tourists anywhere in the world b/c they're all wearing hats, and they only travel in groups. Even in Hawaii which is almost entirely Asian, the Japanese tourists stick out like sore thumbs.