The few prisons that existed before 1960 had been established during the British and Italian colonial administrations. By independence these facilities were in poor condition and were inadequately staffed.

After independence the Somali government included in the constitution an article asserting that criminal punishment must not be an obstacle to convicts' moral reeducation. This article also established a prison organization and emphasized prisoner rehabilitation.

The Somali Penal Code of 1962 effectively stipulated the reorganization of the prison system. The code required that prisoners of all ages work during prison confinement. In return for labor on prison farms, construction projects, and roadbuilding, prisoners received a modest salary, which they could spend in prison canteens or retain until their release. The code also outlawed the imprisonment of juveniles with adults.

By 1969 Somalia's prison system included forty-nine facilities, the best-equipped of which was the Central Prison of Mogadishu. During the 1970s, East Germany helped Somalia build four modern prisons. As opposition to Siad Barre's regime intensified, the country's prisons became so crowded that the government used schools, military and police headquarters, and part of the presidential palace as makeshift jails. Despite criticism by several international humanitarian agencies, the Somali government failed to improve the prison system.