Japan Bike and Hike
If you're looking for an adventure and culture filled hike through Japan, you should check out Japan Bike and Hike in Kunisaki (city), Oita (prefecture), Kyushu (region), Japan.
Joe, the guide, is from Alaska and has lived in Japan for over 25 years. He led our group through some difficult and beautiful mountain trails. For about $250 per day, all meals and accommodations are included. The accommodations included farms, temples, and ryokans (traditional Japanese inns). $250 per day isn't exactly a budget travel, but don't expect to get a hiking guide for much less than that. Besides, for me, it was well worth it.
During the hike, you won't want to escape the ancient Japanese nature and culture all around you. From viewing stone carvings, caves, and shrines to picking raspberries and watching deer frolic through the woods, it is an amazing opportunity to experience rural Japan. And after a long day of hiking through breathtaking mountain views, we would unwind at a local onsen (traditional Japanese bath). If you are going to Japan, you can't miss the opportunity to go to an onsen. Natural hot spring water is just the thing to relax one's muscles.
I highly recommend Japan Bike and Hike if you plan on hiking in Japan.
From journal Summer Backpacking in Japan, 2007