The article analyzes organizational, managerial, and institutional challenges in the development of systemic governance for the implementation of policies with a human rights approach, taking as a case study the Chilean health reform initiated with that approach in 2004. The study integrates a qualitative analysis of legal norms, of managerial instruments and of 40 interviews conducted in 2009 with health executives in three regions of Chile. The findings show that in this reform there is a close connection between incentives and calculations of personal benefit that does not favor agency interdependence. The prevalence of this trait tends to undermine the values of mutual aid and cooperation needed to achieve the integral solutions to social problems that a human rights approach demands. The conclusions reached state, in part, that an uncritical acceptance of management and organization methods inherited from previous institutional reforms often creates contradictions in the development of a governance structure conducive to a human rights approach.