South Africa (SA) is reforming its health system in preparation for an anticipated national health insurance (NHI) scheme that aims to improve the delivery of affordable, equitable, accessible health care. Public health (PH) language is explicit in the policy and skilled PH professionals would be expected to play a key role in its implementation. In South Africa, training of doctors as Public Health Medicine (PHM) specialists is funded by the state, yet there are few positions for PHM specialists in the health services. We explored stakeholders' perspectives about this absence, and their views on PHM specialist' roles and contribution in an era of health reform. A qualitative study was conducted in 2012-13, using in-depth interviews with thematic analysis, which elicited perspectives of 31 key stakeholders nationally reflecting diverse employer and institutional backgrounds. While some were surprised by the absence of PH professionals in SA's health system, most agreed the reason was due to factors internal to the profession, such as its low profile and uncertain identity. External factors such as legislation and political preferences for health managers impacted on the employment of PH professionals. However, given the competencies required to implement an ambitious restructuring of the health sector, all believed that PH and PHM personnel were vital. In view of the health system's dominant curative orientation, embedding PH personnel in the services should ensure that health protection, promotion and prevention strategies will inform health priorities. This study, the first known from a low and middle-income country, contributes to the international literature about the identity and roles of PHM physicians, who are versatile professionals with broad skills-sets. In SA, through consultation with health sector employers about potential roles, curricular redesign and trainee recruitment, PHM can graduate fit-for-purpose specialists to work in a range of institutions to address health system reform.