Recently published childhood vaccination figures by the National Department of Health – showing an alarming drop – may have been skewed by inaccurate population numbers provided by Stats SA, officials admitted to Business Day.
The issue goes to the heart of concerns raised by critics of Stats SA’s Census 2022, which it uses to calculate mid-year population estimates.
Top demographers said that when the census was released in 2024, it was so riddled with anomalies it was not fit for purpose and would compromise future efforts to gauge the impact of government programmes – like childhood vaccination.
Then, last month, the Health Department announced an immunisation crisis, saying more than a third of the country’s infants under the age of one had not received any vaccinations at all.
It said the proportion of so-called “zero dose” babies had skyrocketed from 12% in 2017 to an alarming 36% by April this year, while coverage of the first dose of the six-in-one infant vaccine Hexaxim had plunged from 87% in 2021 to just 60.5% in 2021-25.
The situation put “hundreds of thousands” of babies at risk of severe and potentially life-threatening illnesses, it said, calling for urgent action to increase the vaccination rates.
But several independent sources expressed scepticism about the scale of the declines described in the statement released on 26 August.
Wits professor of vaccinology Shabir Madhi said if the figures were correct, it would imply a total collapse of the country’s immunisation programme.
Additional data subsequently provided by the Health Department to Business Day, which shows the coverage rate for the BCG vaccine against TB had dropped to 66.5% in 2025, was also questionable, he said.
“BCG is given religiously before the baby is discharged (from hospital). Unless there was a BCG stockout – which I’m unaware of – it’s pretty much impossible for BCG coverage to be 66%. There is a major data source issue,” he said.
Immunisation coverage is calculated by dividing the number of doses provided to children in a specific age group (the numerator) divided by the size of the target population (the denominator).
Experts raised concerns about the department’s data sources for both the numerators and denominators used in its calculations. Rather than capturing the details of each vaccinated child on an electronic registry, the Health Department used the number of doses procured by provinces as a proxy, said Madhi.
UCT epidemiologist Leigh Johnson said there was considerable uncertainty regarding the true trend in birth rates in recent years and that the denominators used in the vaccine coverage calculations might therefore be inaccurate.
“It’s not just an issue with the census, as it’s not clear what the trend in births has been in the post-census period,” he said.
The Health Department told Business Day it was confident its data were correct, but there was “some uncertainty regarding the population figures provided by Stats SA”.
“The department has embarked on a process of reviewing the accuracy of these figures, as this may affect coverage estimates,” it said, adding that its figures did not reliably include vaccine administered in the private sector.
Given the uncertainty in the estimates of the vaccine-eligible population, the department’s figures were not a particularly useful indicator of immunisation coverage, said Tom Moultrie, director of the Centre for Actuarial Research at UCT.
He also expressed concern about the lack of reliable independent data sources for the number of annual births, which could be used to estimate the vaccine-eligible population.
The data were previously published in the demographic and health survey conducted by the Health Department and in the national community survey run by Stats SA, but the most recent surveys were done was in 2016, he said.
“The failure of the 2022 census to produce usable data on fertility, which was never released by Stats SA, has compounded our uncertainty,” he said. The lack of empirical data also made it impossible to estimate the extent to which births were under- or over-reported to Home Affairs.
“The considerable uncertainty in the number of births carries significant implications for national service delivery and improving the lives of all people in South Africa.”
At the time of publication, Stats SA had not responded to Business Day’s request for comment.
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