Health Minister Dr Aaron Motsoaledi appointed the council's senior strategist, Dr Sipho Kabane, to act until Zokufa's position as chief executive and registrar is filled.
According to the medical scheme regulator, Kabane has been with the CMS for seven months and has several years’ experience in the public health sector.
Zokufa, who was managing director of the Board of Healthcare Funders, which represents medical schemes and their administrators, resigned from that post in October to head the CMS.
Before Zokufa's appointment, the post had been filled for more than a year by acting registrar Daniel Lehutjo, the council's chief financial officer, following the departure of the former registrar, Dr Monwabisi Gantsho.
Gantsho was suspended in 2014 following allegations by the former curator of Medshield Medical Scheme that he had asked for R3 million of R10 million that Medshield paid to buy its trademark name from the former owners of Medshield’s administration business. Gantsho said last year that, despite a costly R7 million investigation, no evidence of corruption or irregularities in his affairs had been uncovered.