"I am aware of over 30 such cases reported countrywide -- I personally know of 24," said Shaheen Mehtar who heads the unit for infection prevention and control at the Tygerberg Academic Hospital in Cape Town.
"These are all babies whose biological mothers were HIV-negative and who spent some time in hospital," she told AFP.
The Cape Times daily newspaper reported that at least 42 babies and children have been infected with HIV in South African public hospitals, of whom four died, and quoted doctors as blaming poor infection controls.
This included HIV-tainted expressed breast milk being given to hospitalised babies, the re-use of syringes and poor sterilization.
Mark Heywood, spokesman for AIDS lobby group Treatment Action Campaign, said he was aware of more than 40 such infections.
"The overall lack of inspection control policies, procedures and budget means that the problem is probably more widespread," Heywood told AFP.
The health ministry said it had noted the report "with concern", saying infection control was a priority and all hospitals were required to abide by national policies.
"Expressed breast-milk should only be used to feed a baby of the mother who supplied the milk. Pooled expressed breast-milk should not be used because of the risk of transmitting infections," department spokesman Sibani Mngadi said.
The ministry had requested a report with details on specific cases of accidental infection.
Mehtar said she and her colleagues were working with the government to train infection control practitioners, upgrade sterilisation measures, and ensure that all extracted breast milk was pasteurised and labelled with the name of the mother who provided it.
South Africa has one of the world's heaviest burdens of HIV infection with some 5.5 million people infected.