Disease prevention, preservation and improvement of health are the fundamental activities of the public health system and health quality determinants at national level. Thereby, strive is to maximize the efficiency and effectiveness of certain activities which implies a developed reporting system as a prerequisite for measuring achieved results. The public health system in the Republic of Croatia is organized through health and public health institutes at county level. Their activities are aimed at improving the health of the population. The purpose of this paper is to investigate the current reporting and efficiency measurement system and to suggest improvements that will enable the implementation and integration of strategic thinking of organizational units within the public health system. The use of contemporary methods and strategic management tools requires a comprehensive and unified system that ensures information base for monitoring the efficiency of results and the effectiveness of set goals. Accordingly, the objectives of the research are to identify the features of the existing reporting system on the efficiencyand effectiveness of public health services and related organizational structure on a sample of four regional public health institutes and the national institute, whichrepresent the majority of public health services in the Republic of Croatia. The analysis was conducted based on a survey, interviews and available official data for six common organizational units. The major results show discrepancy incertain forms of reporting between the institutes and the inconsistency of organizational solutions for the implementation of particular programs and activities, with an emphasis on internal recording, analysis and reporting. The contribution of this paper is in the critical analysis and the proposed reporting system model as a basis for measuring the efficiency using modern strategic tools, for the purpose of evaluating and developing health care programs, health standards and promoting overall population health.