This paper presents application of an indicator protocol to assessment of current levels of governance capacity of the Specialized Component of Pharmaceutical Services (CEAF) in a state of the South of Brazil. We chose the theoretical referential of 'governance capacity' proposed by Carlos Matus, which reflects in the concepts of management capacity and pharmaceutical service management, due to the perception of a need to overcome the fragmentation and technicist reductionism that we believe has been imposed on the area of pharmaceutical services. Data was collected using the protocol in 74 municipal or state units. The results of the analysis indicate that the currently existing governance capacity needs improvement in all three dimensions that were evaluated, principally in relation to the aspects that seek sustainability of the governance. The model and the protocol used indicate a way forward for governance of pharmaceutical service by proposing a change from the technicist-logistical focus to an emphasis on strategic and political actions, or ones which foster greater participation and autonomy. With these results in hand, it will be possible to develop strategies for improvement of access to medicines in the SUS, in the sense that the CEAF becomes able to guarantee integrality of medicines treatments.