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, Aizuya Inn Tokyo, Alpine Lodge Minakami, Andon Ryokan, Annex Katsuraro Ryokan, Ark Hotel Kyoto, 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, Busena Terrace Resort of Naha, Bed and Breakfast Zen, Bola-Bola Guest House of Kyoto, Ikoi-so Bansuitei Ryokan, Bed and Breakfast Pension Hakadote-mura, Bed and Breakfast Zen, Capsule Inn(Osaka&Kyoto), Center Narita Hotel, Centrair Hotel, Chalet la Niege, Chinryu-an Guesthouse, Chita Guest Inn, Coop Inn, Crown Plaza Tokyo, Dai-Ichi Hotel Ryogoku, Dai-ichi Hotel Tokyo, Daibutsu Ryokan, Ebisu Kyoto, Econo-Inn Kyoto, Edohara Pension at Kuruizawa, Family Inn Fifty’s, Famy Inn Makihari, Fuji Lake Hotel & Resort, Fuji-Hakone Guest House, Fujita Kanko Resorts, Fujiwara Ryokan Nagasaki, Gion Hatanaka Japanese Inn, Gojo Guest House, Grand Hotel New Oji, Green Hill Hotel Kobe, Grove Inn Scala, Guest House Borderless, Guesthouse Hanakiya of Kyoto, Hakodate-Onuma Prince Hotel, Hakuba Mominoki Hotel, Hana To Nagomi No Yado Sankoen, Hakone Hotel, Hakone Hotel Kawakien, Hakone Prince Hotel, Hankyu Hotels, Highland Resort Hotel & Spa, Himeji Castle Hotel, Hiraiwa Ryokan, Hiroshima Prince Hotel, Hokkaido Hotel, Hostel A Silk Tree Yokohama, Hosteling in Japan, Hotel & Accomodation Discounts, Hotel Alpha Kyoto, Hotel Associa Nagoya Terminal, Hotel Associa Toyohashi, Hotel de Yama, Hotel Fukudaya, Hotel Grand Palace, Hotel Granvia Hiroshima, Hotel Granvia-Kyoto, Hotel Halftime Nara, Hotel Iida of Kyoto, Hotel Ilmonte, Hotel Kawanami, Hotel Kazusaya Tokyo, Hotel Kinzankan Tokyo, Hotel Kiyoshi Nagoya, Hotel Kobe Shisyuen, Hotel Listel Shinjuku, Hotel Metropolitan Edmont, Hotel Metropolitan Sendai, Hotel Mt. Fuji, 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 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 Young Inn Kurashiki, Hotel Yuzawa Yuzawa, Ibusuki Seaside Hotel, Ikoisou Bansuiteo Ryokan, Imperial Hotel, Ino’s Place, InterContinental Yokohama the Grand, 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 Ryokan & Hotel Association, Japan Youth Hostels, 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, Kamesaei Ryokan of Nagano, Kanazawa New Grand Hotel, Kaneyoshi Ryokan of Osaka, Karatsu Seaside Hotel, Kariyushi Beach Resort, Kawaguchi-ko Station Inn, Keihana Plaza Hotel, Keio Plaza Hotel, Keio Plaza Hotel Sapporo, Khaosan Tokyo Guest House, Kintestsu International Inbound Travel Guide, Kiroro Resort, Kobe Plaza Hotel, Kodomo No Shiro Hotel, Kurashiki Kokusai Hotel, Kyoto Cheapest Inn, Kyoto Eki-Mae White Hotel, Kyoto Guesthouses, Kyoto Hostel Waraku-An, Kyoto Station Ryokan Seiki, Kyoto Ryokan Watazen, Kyoto Tomato Hostel, Mandarin Oriental Tokyo, Marks Inn Nishi Kawaguchi, Marks Inn Sapporo, McMill House Shimoda, Meitetsu Grand Hotel, Mikuniya Ryokan, Minshuku Kawataniya, Minshuku Rindou-no-ie, Minshuku Sosuke, Miyako Hotels & Resorts, Miyanoshita Fujiya 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, Nikko Minshuku Narusawa Lodge, Nikko Park Lodge, Nikko Pension, Nikko Prince Hotel, Nishitetsu Grand Hotel, Novotel Koshien Osaka West, Oak Hotel Tokyo, Oishiya Ryokan in Ise Shima National Park, Okayama International Villa, Okazaki New Grand Hotel, Okinawa Guest House Lohas Villa, Okinawa Sora House, Okura Frontier Hotel Tsukuba, Okutone Yunoka Hot Springs, Osaka Backpackers’ Hotel Toyoh, Osaka English House, Osaka-Ikeda Fushio-Kaku, Otaru Tenguyama Youth Hostel, Osaka Yamatoya Honten, Palace Hotel Hakone, Palace Hotel Omiya, Park Hyatt Tokyo, Peninsula Hotel Tokyo, Pension Angelica at Mt. Aso, Pension Arashiyama, Pension Grand Papa, Pension Harutugedori, Pension Cosmos at Lake Kawaguchi-ko, Pension Higashiyama, Pension Palette, Pension Sakuraya, Pension Sirogisu, Pension Tengallon Hat, Pension White Pony, Phoenix Seagaia Resort, Prince Hotels, Portopia Hotel, Rakucho Ryokan, Renaissance Hotels, Resort Trust Hotel Group, Righa Roya Hotel Hiroshima, Righa Royal Hotels, Rickshaw Inn, Ritz-Carlton in Osaka, Romantic Ryokans in Japan, Royal Park Hotel, Rusutsu Resort, Ryokan Kashiwara, Ryokan Kamogawa Asakusa, Ryokan Kyoka, 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, Sapporo Grand Hotel, Sapporo Park Hotel, Sapporo Prince Hotel, Satoyu Mukashibanashi Yuzansoo, Sawanoya Ryokan, Sendai Royal Park Hotel, Shalom Hutte Inn, Sheraton Hotels in Japan, Shiga Kanko Hotel Nagano, Shimaya Ryokan Nagano, Shin Matsushima, Shinjuku New City Hotel, Shinjuku 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, Takamatsu City Hotel, Tajimaya Ryokan, Tama Ryokan, The Sapporo Guest House, Takamakura Miyajima Hotels and Shopping, Temple Lodging in Japan, The Tokyo Station Hotel, The Westin Tokyo, The Westin Nagoya Castle, Toba Hotel International, Tokashiki Guesthouse, Tokiwa Hotel, Tokorozawa Park Hotel, Tokyo Backpackers Hostel, Tokyo Central Youth Hostel, Tokyo DisneySea Hotel MiraCosta, Tokyo Hotels, Tokyo Inn, Tokyo and Kyoto International Youth Hostels, Tokyo Japan Hotels, Tokyo Nihonbashi Sumisho Hotel Ningyocho, Tokyo Ryokan, Tokyo Ueno First City Hotel, Tokyo Ueno New Izu Hotel, Tokyo Ueno Touganeya Hotel Japan, Tokyu Hotels, Tour Club Hostel of Kyoto, Towada Prince Hotel, Toyoko-Inn Tokyo, Ueno Terminal Hotel, Uno House of Kyoto, Uotoshi Ryokan, Viento Creation, Villa Park Hotel, Viva Nikko, Watermark Hotel Nagasaki, Whitehouse Inn Kagura, Yaesu Fujiya Hotel, Yamada Bessou, Yamagata Grand Hotel, Yokohama Hostel Village, Yorkshire Farm B&B, Yotsugi Club, Yumoto Fujiya Hotel