Background Within the context of universal health coverage (UHC), South Africa has embarked on a series of health sector reforms. The implementation of the Ideal Clinic Realisation and Maintenance (ICRM) programme is a major UHC reform. Cooperative governance is enshrined in South Africa's Constitution, with health a concurrent competency of national and provincial government. Hence, effective inter-governmental relations (IGR) are essential for the ICRM programme implementation. Aim The aim of the study was to measure the cohesion of IGR, specifically consultation, support and information sharing, across national, provincial and local government health departments in the ICRM programme implementation. Materials and methods Using Provan and Milward's theory on network effectiveness, this study was a whole network design social network analysis (SNA). The study was conducted in two districts in Gauteng (GP) and Mpumalanga (MP) provinces of South Africa. Following informed consent, we used both an interview schedule and a network matrix to collect the social network data from health policy actors in national, provincial and local government. We used UCINET version 6.619 to analyse the SNA data for the overall network cohesion and cohesion within and between the government spheres. Results The social network analysis revealed non-cohesive relationships between the different spheres of government. In both provinces, there was poor consultation in the ICRM programme implementation, illustrated by the low densities of seeking advice (GP = 15.6%; MP = 24.4%) and providing advice (GP = 14.1%; MP = 25.1%). The most cohesive relationships existed within the National Department of Health (density = 66.7%), suggesting that national policy actors sought advice from one another, rather than from the provincial health departments. A density of 2.1% in GP, and 12.5% in MP illustrated the latter. Conclusion The non-cohesive relationships amongst policy actors across government spheres should be addressed in order to realise the benefits of cooperative governance in implementing the ICRM programme.