The commander in chief of the Defense Forces was directly subordinate to the president in matters of military command, principally questions of operations and training. He was responsible for issuing military orders for the preparation and maintenance of readiness of the Defense Forces, for ensuring proper command relationships, and for coordinating all branches of the armed forces in personnel matters. He made recommendations to the president on the organization of military commands and on appointments.

The peacetime defense organization was structured around decentralized and autonomous military areas and districts. There were seven military areas and twenty-three military districts as of early 1989, although the government was considering reducing the number of military areas to five and reducing the districts to between fifteen and seventeen. Each military area comprised two to five military districts. The military area commander, a major general or lieutenant general in peacetime, exercised independent control of all military affairs within his region, including the maintenance of readiness, training of conscripts and reservists, maintenance of a functional mobilization system, wartime logistics preparations, cooperation with civilian authorities, and area defense planning. The commander in chief, who retained planning control of the navy and the air force, could order the commanders of these two services to support a given area command, or he could call upon the general forces of one military area to supply reinforcements to another military area.

The authority of the military district commander was limited in peacetime to planning for crisis or wartime contingencies, operating the conscript and reserve organizations (including call-ups and classification for military service), conducting refresher training, and maintaining the mobilization system. Under wartime conditions, the district commander would mobilize reserve brigades and battalions into the general forces in his district and would command local force operations unless command was assumed by a general forces headquarters.

Data as of December 1988