| Minami-Oda Observatory | Minami | — |
| Minamiaso Luna Observatory | Minamiaso | — |
 Misato Observatory | Distrito de Kaisō | — |
| Mishima observatory | Susono | — |
| Miwa observatory | Manza Onsen Ski Resort | — |
| Miyaki-Argenteus observatory | Miyaki | — |
| Miyasaka Observatory | Miyasaka | — |
| Mizusawa VERA Observatory | — | — |
| Moriyama observatory | Moriyama | — |
| Mount Nyūkasa Optical Observatory | Ina | 1.816 m |
| Mt. Kajigamori observatory | Ōtoyo | — |
| Mui Observatory | — | — |
 Mukai Chiai Children's Science Museum | Tatebayashi | — |
| Murou observatory | Emperador Uda | — |
| Nachi-Katsuura Observatory | Prefectura de Wakayama | 10 m |
| Nagano Observatory | Ōmachi | — |
| Nagatoro observatory | Nagatoro | — |
| Nakagawa observatory | Anan | — |
| Nakagoya Astronomical Observatory “Subaru Dome” | prefectura de Miyazaki | — |
| Nakanoshima Observatory | prefectura de Kagoshima | — |
| Nanyo Observatory | Prefectura de Yamagata | 252 m |
 NAOJ Mizusawa Campus | Ōshū | — |
 Nayoro Municipal Observatory Kitasubaru | Nayoro | — |
 Nichihara Observatory | Tsuwano | — |
| Nishi Kobe observatory | Kobe Bryant | — |
| Nishi-Harima Observatory | Prefectura de Hyōgo | — |
 Nishimino Observatory | Ibigawa | — |
 Nobeyama radio observatory | Minamimaki | 1.350 m |
 Norikura Solar Observatory | Nyūkawa | — |
| NTT Rokko Astronomical Communication Center | Prefectura de Hyōgo | — |
 Obihiro City Children's Hall | Obihiro | — |
| Observatorio Astronómico Dainik | Hikone | 220 m |
 Observatorio Astronómico Nacional de Japón | Mitaka | — |
| Observatorio de Geisei | Geisei | — |
| Observatorio de Hadano | Hadano | 154 m |
 Observatorio de Kitami | Kitami | 165 m |
| Observatorio de Nihondaira | Shimizu-ku | 303 m |
 Observatorio de Saji | Tottori | — |
 Observatorio de Ōizumi | Ōizumi | 38 m |
 Observatorio Gekko | Kannami | 312 m |
| Observatorio Kiso | Prefectura de Nagano | 1.132 m |
| Ochiai observatory | Ochiai | — |
| Oishi Kogen Observatory | Aridagawa | — |
| Oishi observatory | Kimino | — |
| Ojima Observatory | Ojima | — |
| Okayama Astrophysical Observatory | — | — |
| Okutama observatory | Okutama | — |
 Ondake Observatory | Nagasaki | — |