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A popular onsen spot near Tokyo is the Nikko area in Tochigi prefecture such as the Kinugawa onsen. Located two hours from Tokyo, it is easily accessible by bus or train with JR or Tobu line. Kinugawa Park Hotels are one of the best hotels in this area to enjoy an unforgettable week-end with delicious food and amazing facilities. 
Old fashioned, charming Onsen Hotel on the banks of the Hokigawa river in Shiobara onsen. It has been in the same family for 17 generations
Awara Hotel Yagi: Deluxe onsen hotel in Fukui Prefecture
No matter your destination or travel style, the three brands of the Tokyu Hotel chain stand ready to accommodate your needs.
Takayu Onsen: a hot spring getaway in beautiful Fukushima. 
Stay at the Tokachi Makubetsu Onsen Grandvrio Hotel, which is right above the famous Makubetsu Onsen and has a great panoramic view of the Tokachi Plain. 
Matsumoto Ryokan offers incredible food and a lovely bath while you stay in Ginzan Onsen.