The activities of the Corps of Prison and Court Guard are managed, provided with methodologic guidance and supervised by the General Directorate of the Corps. The head of the Corps is represented by the Director General who directly administers the Department of Central Management Support and Communication, the Department of Inspection and Legal Activities, the Department of Human Resources and Social Security, the Department of Preventive-Security Service, the Department of Public Procurement and Project Management and the Active Reserve. The direct superior of the Director General is represented by the Minister of Justice.

The Director General has two deputies. The Deputy Director General for Service Affairs manages the Department of Security, the Department of Pre-trial Detention and Prison Sentence Execution, the Department of Health Care, the Vicariate and the Office of Ecumenical Pastoral Service. The Deputy Director General for Economic Affairs manages the Department of Economics, the Department of Logistics, the Department of Information and Communication Technologies and the Department of Employment, Production and Sales.

At the moment, there are eight combined remand prisons and prisons in Slovakia: In Banská Bystrica, Bratislava, Ilava, Leopoldov, Nitra, Košice, Prešov (with a branch in Sabinov) and in Žilina and nine prisons specialized only for the execution of prison sentence: in Banská Bystrica-Kráľová, Dubnica nad Váhom, Hrnčiarovce nad Parnou, Košice-Šaca, Ružomberok, Želiezovce, Nitra-Chrenová (for women), Levoča (for women) and in Sučany (for juveniles and women). These prison facilities are supplemented by the Prison Hospital and Prison in Trenčín and six open units which are organizational parts of the particular prison facilities.