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The department was concerned at media reports "alleging there have been cases of HIV infection as a result of inadequate infection control measures in some public hospitals", spokesman Sibani Mngadi said in a statement.
Infection control was a priority and all hospitals were required to abide by the National Infection Prevention and Control Policy distributed to all provinces.
The policy requirements included correct and adequate sterilisation of hospital equipment, he said.
Pooled breast-milk banned
Expressed breast-milk should only be used to feed a baby of the mother who supplied the milk, and pooled expressed breast-milk should not be used because of the risk of transmitting infections.
"The national department of health has requested all provinces to report on the progress in the implementation of the National Infection Prevention and Control Policy and on specific cases that have been reported by the Independent Newspapers," Sibani said.
Democratic Alliance spokesman Mike Waters called on Health Minister Manto Tshabalala-Msimang to appoint a task team to investigate the crisis.
Twenty-two babies died from Klebsiella infection at the Mahatma Gandhi Hospital in 2005.
The minister had then set up a high profile task team to investigate the problem, and the hospital had a comprehensive make-over.
Following reports that more than twice this number of babies had been infected with HIV at hospitals around the country because of inadequate infection control measures, the minister needed to respond with the same comprehensive plan, Waters said.
Public hospital stays linked to infection
There had been sporadic reports on the appearance of HIV in babies with HIV-negative mothers, following stays in public hospitals, for several years.
"Now, these reports have been put together - not by the department of health, as one might have expected, but by doctors and the Treatment Action Campaign (TAC).
"It is claimed that 42 babies have been accidentally infected with HIV at public hospitals.
"Without a doubt, there have been many others that have not made it onto this list because there is no requirement on hospitals to monitor this problem or follow up on cases."
The minister should be forced to account for the fact that there was an unmonitored, unrecorded and apparently uncontained plague of HIV infections of babies at state hospitals.
President should intervene
Inkatha Freedom Party KwaZulu-Natal spokesman Bonginkosi Buthelezi called on President Thabo Mbeki to personally intervene.
"Reports such as this one remove all doubts that indeed our health care system is in a crisis and that unless there is an urgent intervention at a Presidential level, it is going to the dogs.
"Not even a single death must be rationalised or justified. How much more than the death of up to 42 babies and children.
"And as if that is not [bad] enough, research says that HIV-infected breast milk is being given to premature babies and dirty syringes are re-used at state hospitals.
"What more must happen before government acknowledges the crisis?"
For the sake of the whole country and the future, the minister should stand up and be counted, or Mbeki should intervene to curb the rot before all was lost, Buthelezi said.
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