The Ministry of Food, Agriculture and Fisheries of Denmark has undergone many changes before assuming its present form.

Prior to the establishment of the Ministry of Agriculture on 22 May 1896, agriculture and fisheries affairs were the responsibility of the Ministry of the Interior.

After the establishment of the Ministry of Agriculture, the interests of both trades were safeguarded there, with the exception of a brief interval from 1929 to 1935, when the Directorate of Fisheries was transferred from the Ministry of Agriculture to the new Ministry of Shipping and Fisheries.

In 1935, the Directorate of Fisheries was again placed under the Ministry of Agriculture, which was named Ministry of Agriculture and Fisheries and assigned responsibility for the interests of the fisheries sector until 13 November 1947, when the Ministry of Fisheries was established as a separate ministry.
 
The Ministry of Agriculture and the Ministry of Fisheries operated independently until 27 September 1994, when they were merged by Royal decree into one ministry called the Ministry of Agriculture and Fisheries.

The organisational integration of the remits of the Ministry of Agriculture and the Ministry of Fisheries was implemented on 1 January 1995.
 
On 30 December 1996, the Ministry of Food, Agriculture and Fisheries was established by Royal decree. 

It meant that the name of the Ministry of Agriculture and Fisheries was changed into that of the new ministry and, at the same time, the National Food Agency as well as matters relating to food and nutrition legislation were transferred from the Ministry of Health.

With the establishment of the Ministry of Food, Agriculture and Fisheries, the responsibility for food administration and food control was placed in one ministry for the purpose of achieving a unified, flexible and coordinated structure.
 
On 2 August 2004, parts of the remit of the Ministry of Food, Agriculture and Fisheries were transferred to the newly established Ministry of Family and Consumer Affairs by Royal decree. The transfer included the Danish Veterinary and Food Administration and the Danish Institute for Food and Veterinary Research.

On 1 January 2007 the Danish Institute of Agricultural Sciences (DIAS) was transferred to the University of Aarhus and named Facultry of Agricultural Sciences. At the same time, the Danish Institute for Fisheries Research (DIFRES) was transferred to the technical University of Denmark.

From 23 November 2007 the Danish Food and Veterinary Administation is again part of the Ministry of Food, Agriculture and Fisheries.