The forerunner of the Agency is the Forest Bureau of the Ministry of Agriculture and Commerce established in 1881. After a major organizational reform in 1947, the Forestry Bureau was established as an extra-ministerial bureau affiliated with the Ministry of Agriculture and Forestry, with the aim of managing national forests and promoting the administration of private forest policies. Until then, the national forests had been jointly managed by three administrative agencies, the Ministry of Agriculture and Forestry, the Ministry of the Interior and the Imperial Household Ministry, but was then integrated into the work of the Bureau. In 1949 the Bureau was renamed the Forestry Agency.

In March 1999, as a part of the fundamental reform of the national forestry management system, organizational structure of regional and local bodies was reviewed and the previous structure of fourteen Regional Forest Office and 229 District Forest Offices was reorganized into seven District Forest Offices and 98 District Forest Offices.