The relevance of the study is determined by the role and place of the legal institution for the protection of human, civil rights, and freedoms as an attribute of the rule of law, the need for proper control and supervisionof their compliance. The Constitution of the Russian Federation proclaims that a person, his rights and freedoms are the highest value, and the state is obliged to recognize, respect and protect the rights and freedoms of man and citizen, judicial protection is guaranteed to everyone. This implies, on the one hand, that everyone is guaranteed to ensure the implementation of the active right to appeal in court decisions, actions or inactions of public authorities and their officials, and on the other hand, verification of compliance with the passive right, which is mainly implemented through control and supervisory procedures. At the same time, in the process of implementing certain functions of the state (in particular, law enforcement), authorized bodies are allowed to apply measures that significantly limit the fundamental constitutional rights and freedoms of a person. An important place among these types of state activities is occupied by operational investigative activities (OIA). In the field of OIA, citizens are often limited in their ability to independently defend their rights and legitimate interests, and therefore a special role in this area is given to the court and the prosecutor’s office. As part of the study, an attempt was made to comprehensively study the theoretical, legal and practical issues of organizing the activities of the prosecutor and the court to protect human and civil rights, the legitimate interests of legal entities in the production of operational investigations, analyze the relationship between prosecutorial and judicial activities, and develop an organic mechanism for their implementation, excluding «mutual substitution» and duplication of competencies.