Adelsman Tours
Illinois based tour operator for first-timers to Japan.
http://www.adelsmantours.com/

All Japan Private Tours and Specialty Services
Offers private full and half day tours in English in Tokyo and the Kansai area, as well as business project coordination and liaising to consulting and specialty shopping.
http://www.kyoto-tokyo-private-tours.com/

Hike Japan
A UK-based company offering walking holidays such as mountain pilgrimage trails, sacred sites, hot springs, and traditional Japanese food and accommodations.
http://www.hikejapan.com/

InsideJapan Tours
Offer small group tours, self-guided packages and fully tailored holidays.
http://www.insidejapantours.com/

J and Y Travel Japan
Agency serving the non-Japanese community specializing in domestic travel.
http://www.jy-travel-japan.com