Police have seen a trend emerge where more children were being killed by their mothers, The Sunday Times reported.
Family violence, child protection and sexual offences unit operational head Brigadier Bafana Linda told the newspaper, "We are seeing more children dying at the hands of their mothers.
"This is extremely worrying. How do the police prevent a child from getting killed in the place where they are presumed to be the most safe?"
The unit secured 499 life sentence convictions over the past financial year alone, Linda said.
Over 1 000 child murders last year
A World Health Organisation study released in May stated that 1018 child murders took place in South Africa in 2009, the newspaper reported.
Over a third, 35.5%, were killed by an acquaintance and nearly 30% by their mothers.
Nearly half, 45.9%, took place in a public space, 34% in the victim's home, while girls were more likely to be killed at home than boys.
Of the children murdered, 43% were cared for by single mothers and 29.8% by both parents.