Although agricultural research in Nigeria started in the late 19 century with the establishment of a botanical garden in Lagos, there was always a problem with the coordination of the research centres and institutes. The botanical garden was part of a network of gardens established under British rule, focusing on the introduction of new crops. In 1903 the Forestry and Botanical Department (renamed Agricultural Department) for southern Nigeria was created. In 1912 this was divided into two regional departments resulting in the establishment of a Department of Agriculture for northern Nigeria. Then in 1914, with Nigeria's unification, the two departments were merged to form a new Department of Agriculture.

Progress was made in terms of infrastructure and human resources resulting in new research stations, more research personnel, and a more technical research program that included plant. breeding and plant pathology. Research continued to focus, however, on export crops like oil palm, rubber, cotton and cocoa. The Forestry and Veterinary Departments were also established in 1914, but only began undertaking research activities in 1920. Fishery research came much later, in 1941, with the establishment of the Fisheries Development Branch by the Department of Agriculture.