Hotels in Japan are essentially clean and orderly. You can stay in a tiny capsule hotel for less than 5000 yen per night, get a business hotel room for less than 10,000 yen per night, stay at a ryokan(Japanese Inn) for somewhat more, or go for the ritzy western hotels in the 30,000 yen range. Love hotels are gaudy looking with a curtain in front to stop gawkers. Even consider a youth hostel. I had a great experience in the one in Miyazaki many years ago. The SIJ Japan directory is the most comprehensive nationwide directory of Japanese visitor hotels and inns on the worldwide web.
Agnes Hotel, Airbnb, Airbnb Faces Difficulties in Japan, Aizuya Inn Tokyo, Alpine Lodge Minakami, ANA Crowne Plaza Kyoto, ANA Crowne Plaza Niigata, Andon Ryokan, Annex Katsuraro Ryokan, Art Hotels, Ashiwada Hotel at Mt. Fuji, Asakusa Tokyo Ryokan & Hostel Toukaisou, Backpackers Fuji in Narita, Asakusa View Hotel, Backpacker’s Hostel Ino’s Place Sapporo, Bed and Breakfast Zen, Bellino Hotel Ichinoseki, Busena Terrace Resort of Naha, Bola-Bola Guest House of Kyoto, British Hills, Bed and Breakfast Pension Hakadote-mura, Buddha Guest House, Capitol Hotel Tokyu, Capsule Inn(Osaka&Kyoto), Center Narita Hotel, Centrair Hotel, Chalet la Niege, Chinryu-an Guesthouse, Coop Inn, Cross Hotel Osaka, Crown Plaza Tokyo, Dai-Ichi Hotel Ryogoku, Dai-ichi Hotel Tokyo, Dai-ichi Hotel Tokyo Seafort, Daibutsu Ryokan, DMC Japan, Ebisu Kyoto, Econo-Inn Kyoto, Edohara Pension at Kuruizawa, Famy Inn Makihari, Fuji Lake Hotel & Resort, Fuji-Hakone Guest House, Fujita Kanko Resorts, Fujiwara Ryokan Nagasaki, Gion Fukuzumi Ryokan, Gion Hatanaka Japanese Inn, Gojo Guest House, Green Hill Hotel Kobe, Grove Inn Scala, Guest House Borderless, Guest House Osaka, Guesthouse Hanakiya of Kyoto, Hakodate-Onuma Prince Hotel, Hakuba Mominoki Hotel, Hakone Hotel, Hakone Hotel Kawakien, Hakone Prince Hotel, Hana Hostel Fukuoka, Haneda Excel Hotel Tokyu, Haneda Royal Park Hotel, Hankyu Hotels, Hearty Inn Ryokan and Hotel Search, Highland Resort Hotel & Spa, Hiraiwa Ryokan, Hiroshima Prince Hotel, Hokkaido Hotel, Hosteling in Japan, Hotel Associa Nagoya Terminal, Hotel Associa Toyohashi, Hotel de Yama, Hotel Fukudaya, Hotel Gracery, Hotel Grand Palace, Hotel Granvia Hiroshima, Hotel Granvia-Kyoto, Hotel Halftime Nara, Hotel Iida of Kyoto, Hotel Ilmonte, Hotel Kazusaya Tokyo, Hotel Kinzankan Tokyo, Hotel Kiyoshi Nagoya, Hotel Listel Shinjuku, Hotel Metropolitan Edmont, Hotel Metropolitan Sendai, Hotel Monterey Sendai, Hotel Nara Club, Hotel New Archaic, Hotel New Azuma, Hotel New Grand Yokohama, Hotel New Gyominso, Hotel New Otani, Hotel New Shohei, Hotel New Ueno, Hotel New Yokosuka, Hotel Nikko Toyohashi, Hotel OkuraGroup, Hotel Patio Dogo, Hotel Roku Roku, Hotel Sendai Plaza, Hotel Station Kyoto, Hotel Suehiro, Hotel Sunlite Tokyo, Hotel Sunroute Asakusa Tokyo, Hotel Taiyo Osaka, Hotel Tateshina Tokyo, Hotel The Manhattan, Hotel Toyota Castle, Hotel Uminonakamichi, Hotel Villa Fontaine, Hotel Village, Hotel Yuzawa Yuzawa, Ibusuki Seaside Hotel, Ikoisou Bansuiteo Ryokan, Imperial Hotel, Ino’s Place, InterContinental Yokohama the Grand, International Guesthouse Azure Narita, Iwasaki Hotels, International Guesthouse Azure, Izu Private Cottage, J-Hoppers Kyoto, JAL Hotels, Japan Alps Kamikochi Miyojinkan, Japan City Hotel Association, Japan Hotel Association, Japan Minshuku Center, Japan Ryokan Association, Japan Youth Hostels, Japanese Eco-Guesthouse Kunelasob, Japanese Guest Houses, Juyoh Hotel in Tokyo, K’s House Hakuba Alps, K’s House Kyoto, K’s House Mt. Fuji, K’s House Tokyo, Kaigetsu Inn, Kabutoya Inn, Kamakura Park Hotel, Kamesei Ryokan of Nagano, Kanaya Hotel, Kanazawa New Grand Hotel, Kaneyoshi Ryokan of Osaka, Kapalua Pension, Karatsu Seaside Hotel, Kariyushi Beach Resort, Karuizawa Pension Kapalua, Kawaguchi-ko Station Inn, Keihana Plaza Hotel, Keio Plaza Hotel, Keio Plaza Hotel Sapporo, Keisei Hotel Miramare, Khaosan Tokyo Guest House, Kichijoji Dai-ichi Hotel, Kiroro Resort, Kobe City Gardens Hotel, Kobe Plaza Hotel, Kodomo No Shiro Hotel, Kurashiki Kokusai Hotel, Kushiro Prince Hotel, Kyoto Cheapest Inn, Kyoto Green Peace Guesthouse, Kyoto Guesthouses, Kyoto Hostel Waraku-An, Kyoto Ryokan Karaku, Kyoto Station Ryokan Seiki, Kyoto Ryokan Watazen, Kyoto Tomato Hostel, Kyoto Tower Hotel, Lake Biwa Otsu Prince Hotel, Lotte City Hotel Kinshicho, Mandarin Oriental Tokyo, Manza Prince Hotel, Marks Inn Sapporo, McMill House Shimoda, Meitetsu Grand Hotel, Meitetsu Inuyama Hotel, Meitetsu Toyota Hotel, Mikuniya Ryokan, Minshuku Minami Sanriku, Minshuku Kawataniya, Minshuku Rindou-no-ie, Minshuku Sosuke, Mito Plaza Hotel, Mitsui Garden Hotel Yotsuya, Miyako Hotels & Resorts, Miyanoshita Fujiya Hotel, Morioka Grand Hotel, Mt. Fuji Rising Sun Inn, Nagaoka Grand Hotel, Nagasaki International Hostel Akari, Nagoya Kanko Hotel, Nagoya Marriott Associa Hotel, Nagoya Tokyu Hotel, National Park Resort Villages, New Oriental Hotel, New Sanno Hotel, Nichinankaigan Nango Prince Hotel, Niigata Grand Hotel, Nikko Minshuku Narusawa Lodge, Nikko Park Lodge, Nikko Pension, Nikko Prince Hotel, Nippon Daira Hotel, Nishitetsu Grand Hotel, Novotel Koshien Osaka West, Oak Hotel Tokyo, Ochanomizu St. Hills Hotel, Oishiya Ryokan in Ise Shima National Park, Okayama International Villa, Okazaki New Grand Hotel, Okinawa Guest House Lohas Villa, Okinawa Kariyushi Beach Resort Ocean Spa, Okinawa Sora House, Okinawa Spa Resort Exes, Okura Frontier Hotel Tsukuba, Osaka Backpackers’ Hotel Toyoh, Osaka English House, Osaka-Ikeda Fushio-Kaku, Osaka Mariott Miyako Hotel, Osaka Yamatoya Honten, Otaru Tenguyama Youth Hostel, Otarunai Backpackers’ Hostel, Morinoki, Pacific Resorts, Palace Hotel Hakone, Palace Hotel Omiya, Palace Hotel Tachikawa, Park Hyatt Tokyo, Peninsula Hotel Tokyo, Pension Arashiyama, Pension Grand Papa, Pension Harutugedori, Pension Cosmos at Lake Kawaguchi-ko, Pension Higashiyama, Pension Palette, Pension Sakuraya, Pension Tengallon Hat, Pension White Pony, Phoenix Seagaia Resort, Portopia Hotel, Prince Hotels, Prince Hakone Lake Ashinoko, Prince Park Tower Tokyo, Rakucho Ryokan, Renaissance Hotels, Resort Trust Hotel Group, Richmond Hotel Premier Sendai Ekimae, Righa Roya Hotel Hiroshima, Righa Royal Hotels, Rickshaw Inn, Ritz-Carlton in Osaka, Riviera Resort, Romantic Ryokans in Japan, Royal Park Hotel, Rusutsu Resort, Ryokan Kashiwara, Ryokan Kamogawa Asakusa, Ryokan Kyoka, Ryokan Meiryu Nagoya, Ryokan Nissho-besso Kyoto, Ryokan Ryumeikan-Honten Tokyo, Ryokan Sakura, Ryokan Seifu-so Nagano, Ryokan Shosenkaku, Ryokan Seiru Hida Takeyama, Ryokan Seryo, Ryokans in the Kinki Region, Sakura Hotel Tokyo, Sannomiya Terminal Hotel, Sapporo Grand Hotel, Sapporo Park Hotel, Sapporo Prince Hotel, Satoyu Mukashibanashi Yuzansoo, Sawanoya Ryokan, Sendai Royal Park Hotel, Senri Hankyu Hotel, Setouchi Kojima Hotel, Shalom Hutte Inn, Shiba Park Hotel, Sheraton Hotels in Japan, Sheraton Miyako Hotel Tokyo, Shibuya Tokyu Rei Hotel, Shiga Kanko Hotel Nagano, Shimaya Ryokan Nagano, Shimoda Prince Hotel, Shimonoseki Grand Hotel, Shinjuku Hotel Park Inn, Shinjuku New City Hotel, Shiodome Tokyo Royal Park Hotel, Shirogane Mountain Lodge, Sierra Hakuba Resort, Solar Cafe Guest House, Solare Hotels and Resorts, SPA Hostel Khaosan Beppu, St. Hills Hotel, Stella Resort Okinawa Guesthouse, Sunsky Hotel, Taisho Ryokan Nara, Taito Ryokan, Takakura Hotel, Takamatsu City Hotel, Tajimaya Ryokan, Tama Ryokan, The Sapporo Guest House, Takamakura Miyajima Hotels and Shopping, Temple Lodging in Japan, The Strings by Intercontinental Tokyo, The Tokyo Station Hotel, The Westin Miyako Tokyo, The Westin Tokyo, Toba Hotel International, Tobu Hotel Levant Tokyo, Tokashiki Guesthouse, Tokiwa Hotel, Tokorozawa Park Hotel, Tokyo Backpackers Hostel, Tokyo Central Youth Hostel, Tokyo DisneySea Hotel MiraCosta, Tokyo Dome Hotel, Tokyo Green Hotel Korakuen, Tokyo Hotel Nihonbashi Villa, Tokyo Hotels, Tokyo Inn, Tokyo and Kyoto International Youth Hostels, Tokyo Japan Hotels, Tokyo Mariott Hotel, Tokyo Nihonbashi Sumisho Hotel Ningyocho, Tokyo Ryokan, Tokyo Ueno First City Hotel, Tokyo Ueno New Izu Hotel, Tokyo Ueno Touganeya Hotel Japan, Tokyu Hotels, Towada Prince Hotel, Toyokan Inn, Toyoko-Inn, Ueno Terminal Hotel, Unizo Inn Asakusa, Uno House of Kyoto, Unzen Kanko Hotel, Uotoshi Ryokan, Urvest Hotel Kamata East Tokyo, Utsunomiya Grand Hotel, Vessel Hotels, Villa Park Hotel, Watermark Hotel Nagasaki, Whitealbum Osaka Guest House Budget Hostel, Whitehouse Inn Kagura, Yadoya Guesthouse, Yaesu Fujiya Hotel, Yamada Bessou, Yamagata Grand Hotel, Yokohama Bay Sheraton Hotel and Towers, Yokohama Hostel Village, Yokohama Royal Park Hotel, Yorkshire Farm B&B, Yotsugi Club, Yumoto Fujiya Hotel