Paper presents the problem of designing the organizational structure and operating model for National Security System of the Republic of Poland (SEN RP). Classical and modern organizational structures have been taken into consideration. These structures provide mechanisms to increase the flexibility and coordination of the functioning of such organizations. Author has introduced the idea of the rational model of organizational structure of the system, consisting of parts of relatively constant (stable) and highly flexible. The required level of integration and standardization of processes carried out within the newly proposed organizational structures SEN RP also have been determined.