| Adati observatory | Minamisōma | — |
| Ageo observatory | Ageo | — |
| Akashina observatory | Akashina | — |
| Akeno Giant Air Shower Array | Akeno | — |
| Akou observatory | Akō | — |
 Asahikawa observatory | Asahikawa | — |
 Asahikawa Science Center "Sci-Pal" | Asahikawa | — |
 Asama Volcano Observatory | — | 1.406 m |
| Aso Volcanological Laboratory | Minamiaso | — |
| ASTRO-A | — | — |
| Astronomical Observatory Cosmos Dome | Prefectura de Yamagata | — |
| Ayabe City Astronomical Museum | Ayabe | — |
| Ayabe observatory | Ayabe | — |
| Bibai observatory | Bibai | — |
 Centro Spaceguard de Bisei | Bisei | 427 m |
| Chichibu Observatory | Chichibu | 800 m |
| Chirorin observatory | Otari | — |
| Daito Cosmic Park Hoshi no Kuni | Gojō | — |
| Estación sismológica de Mikazukiyama | Ogasawara | — |
| Estación Yakiimo | Shimizu-ku | — |
| Fujieda observatory | Fujieda | — |
| Fukuchiyama and Kannabe observatory | Fukuchiyama | — |
| Fukushima Jōdodaira Astronomical Observatory | Fukushima | — |
| Furukawa observatory | Hida | — |
 Geospatial Information Authority of Japan | Kitasato | — |
 Gifu Astronomical Observatory | Gifu | — |
| Go-Chome and Kobe-Suma observatory | Kobe Bryant | — |
| Gumma Astronomical observatory | Takayama Onsen Fureai Plaza | — |
 Gunma Astronomical Observatory | Takayama (Gunma) | — |
 Hamamatsu City Observatory | Minami-ku | — |
| Hamamatsu-Yuto observatory | Hamamatsu | — |
| Hatamae observatory | Sendai | — |
 Haterumajima Astronomical Observatory Tower | Taketomi | — |
| Hida Observatory | Takayama | — |
| Hidaka Observatory | Hidaka | — |
| Higashi-Hiroshima Observatory | Higashihiroshima | — |
| Hill Town Local Studies Museum “Miku” | Prefectura de Hokkaido | — |
| Hirao Observatory | Hirao | — |
| Hiratsuka observatory | Hiratsuka | — |
| Honjo observatory | Honjō | — |
 Hoshi no Mura Observatory | Tamura | — |
 Hyper-Kamiokande | Hida | — |
| Iga-Ueno observatory | Tsuge Station | — |
| Iitate Planetary Radio Telescope | Prefectura de Fukushima | — |
| Inagawa Observatory | Distrito de Kawabe | — |
| Institute of Seismology and Volcanology, Faculty of Sciences, Kyushu University | Shimabara | — |
 Ishigakijima Astronomical Observatory | Ishigaki | 200 m |
| Ishiki observatory | Ishiki | — |