Introduction:The Ministry of Health influences the executive organizations through the high councils and the decision-making system. It is necessary to adopt an inter-sectoral cooperation approach, seek appropriate support for interacting with these councils, focus on the health taken decisions, and analyze their current situation. This study aimed to investigate the challenges and barriers to the interaction of high councils of health with the Iran Ministry of Health.Material & Methods: The present study is a field-based qualitative study that was conducted to analyze the current situation of the High Councils. Data were collected through interviews, group discussion sessions, and document analysis. To collect the data, 23 interviews and 2 focus group sessions were conducted using purposive sampling. The obtained data were then analyzed using MAXQDA software (version 10). (Ethic code: 162432750) Findings: The results of the study showed that in terms of activity, the elected high councils are divided into three categories of active, semi-active, and inactive. Challenges facing these councils include lack of financial and human resources, inadequate structure and organization, non-transparent rules and regulations, lack of executive guarantees, poor planning and cross-sectoral coordination, lack of monitoring and evaluation system, low level of awareness and attitude of policy makers and managers about health, poor leadership of the Ministry of Health, and finally the lack of a health appendix in approvals. The improvement of the performance of high councils in applying the health appendix to approvals can be achieved through such interventions as 1. Policy interventions, 2. Executive structure interventions, and 3. Culture building and advocacy. Discussion & Conclusion: According to the results of the study, it is necessary for the health system to develop inter-sectoral cooperation and seek appropriate support from high councils in order to fairly improve community health indicators, take action to reduce barriers to interaction through policy, executive, culturebuilding, and advocacy interventions.