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Daftar danau di Jepang diurutkan berdasarkan luas permukaan.

Peringkat	Nama	Wilayah	Prefektur¹	Munisipalitas	Air	Area (km²)	Kedalaman Maks (m)	Ketinggian (m)	Volume (km³)
1	Biwa	Kansai	Shiga	Ōtsu, Kusatsu, Higashi-Ōmi, Hikone Nagahama, Moriyama, Ōmi-Hachiman Takashima, Yasu, Maibara	Tawar	670.3	103.8	85	27.5
2	Kasumigaura	Kantō	Ibaraki	Tsuchiura, Ishioka, Omitama, Inashiki Ami, Kasumigaura, Namegata, Itako, Miho	Tawar	167.6	7.10	0	0.85
3	Saroma	Hokkaidō	Abashiri	Kitami, Saroma, Yūbetsu	Payau	151.9	19.6	0	1.3
4	Inawashiro	Tōhoku	Fukushima	Aizuwakamatsu, Inawashiro, Kōriyama	Tawar	103.3	94.6	514	5.40
5	Nakaumi	San'in	Shimane Tottori	Matsue, Yonago, Yasugi Sakaiminato, Higashi-Izumo	Payau	86.2	17.1	0	0.47
6	Kussharo	Hokkaidō	Kushiro	Teshikaga	Tawar	79.3	117.5	121	2.25
7	Shinji	San'in	Shimane	Matsue, Izumo, Hikawa	Payau	79.1	6.0	0	0.34
8	Shikotsu	Hokkaidō	Ishikari	Chitose	Tawar	78.4	360.1	247	20.9
9	Tōya	Hokkaidō	Iburi	Tōyako, Sōbetsu	Tawar	70.7	179.9	84	8.19
10	Hamana	Tōkai	Shizuoka	Hamamatsu, Kosai, Arai	Payau	65.0	13.1	0	0.35
11	Ogawara	Tōhoku	Aomori	Misawa, Tōhoku, Rokkasho	Payau	62.2	24.4	0	0.714
12	Towada	Tōhoku	Aomori Akita	Towada, Kosaka	Tawar	61.0	326.8	400	4.19
13	Notoro	Hokkaidō	Abashiri	Abashiri	Payau	58.4	23.1	0	0.5
14	Fūren	Hokkaidō	Nemuro	Nemuro, Betsukai	Payau	57.5	13.0	0	0.0564
15	Kitaura	Kantō	Ibaraki	Kashima, Hokota, Namegata, Itako	Tawar	35.2	7.0	0	0.18
16	Abashiri	Hokkaidō	Abashiri	Abashiri, Ōzora	Payau	32.3	16.1	0	0.2
17	Akkeshi	Hokkaidō	Kushiro	Akkeshi, Hokkaidō	Tawar	32.3	11.0	0
18	Hachirō	Tōhoku	Akita	Katagami, Oga, Gojōme, Ikawa, Ōgata	Tawar	27.7	12.0	0
19	Tazawa	Tōhoku	Akita	Senboku	Tawar	25.8	423.4	249	7.2
20	Mashū	Hokkaidō	Kushiro	Teshikaga	Tawar	19.2	211.4	351
21	Jūsan	Tōhoku	Aomori	Goshogawara, Tsugaru, Nakadomari	Payau	18.1	1.5	0
22	Kutcharo	Hokkaidō	Sōya	Hamatonbetsu	Tawar	13.3	3.3	0	0.014
23	Suwa	Chūbu	Nagano	Okaya, Suwa, Shimo-Suwa	Tawar	13.3	7.6	759	0.06135
24	Akan	Hokkaidō	Kushiro	Kushiro	Tawar	13.0	44.8	420	0.249
25	Chūzenji	Kantō	Tochigi	Nikkō	Tawar	11.8	163.0	1269	1.1
26	Inba	Kantō	Chiba	Yachiyo, Sakura, Narita, Inzai, Shisui, Sakae	Tawar	11.55	2.5	2.5	0.0277
27	Ikeda	Kyūshū	Kagoshima	Ibusuki	Tawar	10.9	233.0	66	1.38
28	Hibara	Tōhoku	Fukushima	Kitashiobara	Tawar	10.7	30.5	822	0.13
29	Ashi	Kantō	Kanagawa	Hakone	Tawar	7.03	43.5	723
30	Kuttara	Hokkaidō	Iburi	Shiraoi	Tawar	4.68	148	258	0.491

1) Untuk danau di wilayah Hokkaido, Subprefektur terdaftar

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(dalam bahasa Jepang) The Japanese Ministry of Land, Infrastructure, and Transport - Significant Lakes of Japan
(dalam bahasa Jepang) Wikipedia - List of lakes in Japan

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