It is well known that war suddenly disrupts the legal order and suspends, within the limits of its action, the proper application of the rules of law. The rules that are developed and operate in times of peace are, largely, ineffective in times of armed conflict, and the rules adopted in times of war are nullified when peace is restored. This situation largely affects the investigation and detection of crime. The investigation of war crimes requires the maximum concentration of professional efforts and capacities, appropriate qualifications and experience in this field, as well as knowledge of the organization of law enforcement, its planning, the operational implementation of special investigative measures and prosecutorial actions. The implementation of organizational measures in this area will contribute to the efficiency of the war crimes investigation process and the collection of evidence of war crimes committed by the belligerent parties to the armed conflict. This study focuses on the system, specifics and content of measures for the organization of war crimes investigations, which are in fact an important component of qualitative investigations, their detection and the punishment of war criminals.