The activities of the Corps of Prison and Court Guard are directed, organized, methodologically guided, and supervised by the Directorate General of the Corps of Prison and Court Guard. It is headed by the Director General, who directly manages the Department of Inspection and Legal and Organizational Affairs, the Department of Human Resources and Social Affairs, the Department of Preventive and Security Services, the Chaplain, and the Office of the Ecumenical Pastoral Service. The Director General reports directly to the Minister of Justice.

Reporting directly to the Director General are two Deputy Directors General and the Project and IT Management Officer. The Deputy Director General for Service Affairs oversees the Department of Security, the Department of Remand and Prison Sentence Execution, and the Department of Health Care. The Deputy Director General for Economic Affairs is in charge of the Department of Economics, the Department of Logistics, the Department of Public Procurement, and the Department of Employment, Production and Sales. The Project and IT Management Officer supervises the Department of Projects and Strategies and the Department of Security and Information Systems Operations.

There are currently eight combined remand and prison sentence execution prisons in Slovakia: in Banská Bystrica, Bratislava, Ilava, Leopoldov, Nitra, Košice, Prešov (with a branch in Sabinov), and Žilina, and nine prisons specialized solely in the execution of prison sentences: in Banská Bystrica-Kráľová, Dubnica nad Váhom, Hrnčiarovce nad Parnou, Košice-Šaca, Ružomberok, Želiezovce, Nitra-Chrenová (for women), Levoča (for women), and Sučany (for juveniles and women). These prisons are complemented by a hospital for remand and sentenced prisoners in Trenčín and seven open units, which are organizational parts of individual prisons.