Building heavily on the Health in All Policies (HiAP) approach, Norway implemented the Public Health Act in 2012 to reduce social inequalities in health. Local public health coordinators (PHCs) at municipal levels were seen as tools to provide local intersectoral public health work. In this study, we examine factors related to intersectoral agency and if intersectoral work is understood as relevant to securing social justice in local policy outcomes. A national web-based survey in 2019 of all Norwegian PHCs (n = 428) was conducted with a response rate of 60%. Data were analysed through multiple linear regression, hierarchical regression modelling and structural equation modelling. Neither factors relating to community contexts nor individual characteristics were associated with intersectoral agency. Organisational factors, especially position size, being organised at the top level and having a job description, were significantly associated with perceptions of intersectoral agency. PHCs seeing themselves as intersectoral agents also found themselves able to affect annual budgets and policy outcomes. We conclude that municipal PHC positions can be important HiAP tools in local public health policies. However, organisational factors affect how PHCs perceive their influence and role in the municipal organisation and thereby their possibilities to influence local policymaking through intersectoral agency.