Little is known about the organizational factors involved in policy creation and programs implementation aimed at reducing maternal mortality in Madagascar. A qualitative case study was performed to investigate organizational factors influencing the health system's capacity to elaborate and implement maternal mortality reduction programs. Semi-structured interviews were conducted with 53 participants. A conceptual framework based on Gamson's coalition theory and Hinings and Greenwood's archetypes concept was used. Three major conclusions emerge: the Ministry of Health is a poor leader in the development of national strategies, due to its dependency on external financial resources and expertise, and because of poor transmission of key information from the field; at a meso level (regions and districts), the capacity to adapt programs is highly dependent on the collaboration with NGOs; at the micro level, there are few incentives provided to field workers to participate in a collective effort and little attempt to exploit complementarities between scare resources. The Madagascar health system should consider the need for improvement in data analysis capacity, and implementing behavior-changing tools suitable for stimulating providers who work inside and outside the health care system, to participate to a coordinated collective effort.