Plans by Parliament to replace the Medicines Control Council (MCC) with a government body overseen by the health minister have come under fire from the South African Medical Association (Sama) and the Treatment Action Campaign (TAC).
The Medicines and Related Substances Amendment Bill is being debated in Parliament.
It gives the minister of health power to decide whether new medicines can be registered.
Sama chairman Kgosi Letlape said if the bill was passed, it would be "an absolute disaster".
"Registering new medicines that are useful for the community will be subjected to one person's approval," he told Sowetan.
"The registration process already takes too long and this will create even more delays."
He said that Sama believed that medicines should be registered based on "a scientific process".
Thami Mseleku, director-general of health, reportedly told Parliament this week that the minister would register only medicines that had been certified as effective "if it is in the public interest to do so".
The TAC told Parliament this week the bill would pave the way for the minister to allow the sale and provision of untested "treatments" and "cures". It said that it could be used to block new and effective anti-retroviral medications from being registered.
But Minister Manto Tshabalala-Msimang's spokesman Sibani Mngadi said that "the act does not remove the scientific evaluation or verification of medicines. The new agency will be quicker than the current registration environment."
Mngadi said the new government agency would have more staff than the MCC and it would have "more flexibility" to set better salaries.
Mngadi said the new government agency would be similar to the Food and Drug Agency in the US.