To ensure the quality of nuclear disaster medical care, facilities are being developed worldwide in the event of a nuclear disaster. However, the relationship between the existence of permanent facilities and the presence or absence of facility operation manuals has not been clarified in the field of nuclear disaster medicine. This study aims to determine the relationships between the existence of permanent facilities, the presence or absence of facility operation manuals and the number of years elapsed since a facility was designated for nuclear disaster medicine. In September 2021, 26 facilities responded to an online questionnaire of the 53 facilities of nuclear disaster-related hospitals (valid response rate of 49.1%) in Japan. The existence of permanent facilities for nuclear disaster medicine was significantly higher in facilities with fewer years of designation than in those with more years of designation. The existence of permanent facilities for nuclear disaster medicine facilitated the organisational awareness of a nuclear disaster, as evidenced by the availability of manuals, regardless of the number of years elapsed since designation. In conclusion, the study suggests that the existence of permanent facilities is an important factor for organisational preparedness for a nuclear disaster.