The political institution responsible for the penitentiary system is the Ministry of the Interior.

The organization that administers it directly is the National Rehabilitation Institute (INR), created by the 2010 Finance Act (Law No. 18.719). The INR directs the 29 prison units that make up the system.

To date, and despite the proposed laws introduced in Parliament, no organic law establishing the INR as a decentralized service of the State has been promulgated. For this reason, the system is organized in accordance with the provisions of Decree-Law No. 14.470 of 1975, dating from the period of civil and military dictatorship. To date, no regulation has been adopted to replace it.

Penitentiary units are classified as:

• Maximum security units;
• Medium security units;
• Units with minimum security and maximum confidence.

The Admission, Diagnosis and Assignment Unit, the “gateway” of the system, is in charge of the reception of male senior prisoners, their classification and their assignment in the different units. In practice, it turns out that the National Transfer Council, depending on the places available in the different units, dictates the assignment.

The only unit to exclusively receive sentenced male prisoners is Unit 6 (Punta de Rieles), with a capacity of 650 people. The main unit for receiving female prisoners is Unit 5, in which the accused and convicted are not separated. Unit 9, located in the same building as Unit 5, accommodates women with young children, but there is not enough accommodation.

All Maximum and Medium Security Units have surveillance perimeters controlled by soldiers from the Ministry of Defence.

In the case of minors in conflict with the criminal law, there is only one centre for teenage girls and one centre for boys aged 14 to 15. The remaining 12 centres accommodate boys aged 15 to 18 who are subject to preventive and custodial measures. In general, it equally accommodates some major inmates (around 100 on average). It is often the case where a minor escapes from the institution, is sentenced to an adult prison sentence, and then has to return to the juvenile centre in order to finish serving the sentence for the crime committed as a minor. Prison experts have recommended on many occasions the establishment of an intermediate penal system between the juvenile system and the adult penitentiary system, but so far government authorities have not heard them.

No units are reserved for prisoners with severe psychiatric disorders. In fact, people who are declared criminally irresponsible do not enter the penal system.

A process of reforms, still in progress and presenting significant difficulties, was launched in 2010, the fruit of a multi-party agreement. One of these reforms allows, for the first time in the country’s prison history, to bring all prisons together in one institution: the INR. In addition, this reform process includes among its objectives the “depoliciarization” of prisons and the creation of a new type of prison officials - penitentiary operators - with civilian status and training neither police nor military. This process is still on-going and is lagging behind the original objectives. Many prison officials show their refusal, and sometimes obstruct the implementation of these reforms, especially police personnel.