BACKGROUND: Primary health centres (PHCs) in Nigeria suffer critical shortages of health workers, aggravated by chronic absenteeism that has been attributed to insufficient resources to govern the system and adequately meet their welfare needs. However, the political drivers of this phenomenon are rarely considered. We have asked how political power and networks influence absenteeism in the Nigerian health sector, information that can inform the development of holistic solutions. METHODS: Data were obtained from in-depth interviews with three health administrators, 30 health workers and 6 health facility committee chairmen in 15 PHCs in Enugu State, Nigeria. Our analysis explored how political configurations and the resulting distribution of power influence absenteeism in Nigeria's health systems. RESULTS: We found that health workers leverage social networks with powerful and politically connected individuals to be absent from duty and escape sanctions. This reflects the dominant political settlement. Thus, the formal governance structures that are meant to regulate the operations of the health system are weak, thereby allowing powerful individuals to exert influence using informal means. As a result, health managers do not confront absentees who have a relationship with political actors for fear of repercussions, including retaliation through informal pressure. In addition, we found that while health system structures cannot effectively handle widespread absenteeism, networks of local actors, when interested and involved, could address absenteeism by enabling health managers to call politically connected staff to order. CONCLUSION: The formal governance mechanisms to reduce absenteeism are insufficient, and building alliances (often informal) with local elites interested in improving service delivery locally may help to reduce interference by other powerful actors.