The anti-retroviral drug is said to reduce MTCT by 50%
Campaigners have expressed alarm at the possibility that the South African Government could withdraw its approval for the anti-Aids drug Nevirapine.
Nevirapine prevents HIV-positive pregnant mothers passing on their infection to their child.
A single dose of the drug given at the onset of labour, and a single dose to the newborn within 72 hours of birth, has been shown to reduce mother-to-child transmission (MTCT) of the virus by 50%.
But the South African Medicine Control Council (MCC) has expressed doubts over its safety.
The MCC's announcement comes just days after the World Health Organisation (WHO) reconfirmed its support for the drug to be included in the minimum standard package of care for HIV-positive women and their children.
Nevirapine became the first anti-retroviral drug approved for use in the country in 2002 after activists won a court order forcing the government to provide it for HIV-positive mothers.
South African activists have long campaigned for anti-retroviral drugs to be made freely available in South African hospitals.
But the government says that the drugs are expensive and has preferred to emphasise the importance of nutrition and poverty reduction. It also says it prefers prevention over treatment.
The MCC is asking the German manufacturers of Nevirapine, Boehringer Ingelheim, to provide new scientific proof of the drug's efficacy within 90 days.
But the council's decision has shocked the company, which says that it has been providing Nevirapine free for maternal HIV treatment in several South African provinces and had no indication of any safety problems.
The company told BBC News Online that it had given the MCC as much supporting evidence as it could and would continue to co-operate with them.
"However, should the MCC continue to consider these reporting and documentation issues as grounds for deregistration that is their prerogative.
"At least we shall have used our best efforts to ensure that a simple and potentially life-saving medicine will not be withheld from those in need," said spokesperson Julia Kleinmann.
Siphokazi Mthathi, of the campaigning group, Treatment Action Campaign (TAC), told BBC News Online that the MCC's move is undermining the work of their Aids campaign and the trust the people had started to build in the treatment programme.
The WHO said in early July that it supported the use of Nevirapine.
1.8m children may lose a parent by 2010 without anti-Aids drugs
The body said it agrees that there is no evidence that scientific data from a 1997 Ugandan study "demonstrating the safety and efficacy of Nevirapine is invalid".
MCC registrar Precious Matsoso told the French news agency AFP on Wednesday that the council had conducted its own investigation and concluded that a clinical trial in Uganda had not met the MCC's registration criteria.
Ms Mthathi said that while Aids campaigners support the provision of the necessary documents demanded from Boehringer Ingelheim, the MMC should not use the Uganda study as an excuse to ban the drug, "because South Africa has its own study which started in 2001 with 6,000 mothers, receiving the treatment showing no cause for alarm".
The MCC action has created fear and confusion among South Africans, leaving those on the programme sad and demotivated, she said.
The TAC says that 1.8 million additional children will lose a parent by 2010 if the anti-Aids drugs are not provided.
South Africa has more HIV-positive people than any other country in the world. Activists say some 600 South Africans die from Aids-related diseases each day.
The council's announcement is now likely to dominate the conference of South Africa's National Aids Congress next week in Durban.