The meteorological services in Japan were launched in 1875 when the Tokyo Meteorological Observatory was established inside the Geodesy Division of Chiriryo (Geography Hall) of the Ministry of Interior and started making seismic observations and meteorological forecasts three times a day on the premises of the Chiriryo. The Observatory was renamed the Central Meteorological Observatory in 1887. In 1895, it was transferred to the Ministry of Education, and in 1943 transferred to the Ministry of Transport and Communications. In1956, the status of the Observatory was raised to an external organ of the Ministry of Transport, and its name was changed to the Japan Meteorological Agency.

The Agency became an external organ of the Ministry of Land, Infrastructure and Transport, following the reorganization of central government ministries and agencies in January 2001.