About 16,000 children have disappeared in the past 18 years, and more than 4,000 have never been found.
These shocking figures have been gleaned from police statistics by Unisa criminologist and former Hawks organised crime investigator Marcel van der Watt.
NGOs trying to find missing children say they face increased caseloads, a dwindling success rate and the grim reality that one in four victims is found dead.
Police in Mpumalanga, the Western Cape and the Eastern Cape are concerned about an increase in child abductions, which account for an estimated one in eight of Missing Children SA's most recent cases.
Police say most kidnappings happen when children are alone in the street or walking home without adult supervision.
Eastern Cape premier Phumulo Masualle said four children from Whittlesea, near Queenstown, were abducted with the alleged collusion of relatives, who traded the children for groceries.
Masualle also implicated churches.
"Certain churches are being used as a disguise in perpetrating this crime," he said.
According to police data provided to Van der Watt for his PhD on human trafficking, the provinces with most child disappearances were Gauteng, the Western Cape and KwaZulu-Natal.
But the figures were unreliable. Van der Watt's research found that police sifted through case files of missing people by hand to verify the number on their database because these had been filed with wanted suspects.
Van der Watt said it had taken over a year to get figures from the police.
"There is no data on the number of people reported missing, found, or the reasons and circumstances for their disappearance," he said.
"There is no information on the ages, gender or race, or how many missing persons cases translate into police inquiries or criminal cases or the outcomes of these.
"Available statistics are not even remotely an accurate reflection of the state of affairs regarding the missing children."
Maj-Gen Bafana Linda, national head of the family violence, child protection and sexual offences (FCS) unit, said he could not comment on Van der Watt's research.
Asked about missing and wanted people sharing a database, and why crime statistics had not isolated kidnappings, abductions and missing persons cases, he said he wanted to "shy away from stats and databases".
As far as he knew, child kidnappings were not increasing.
"What I can say is that the number of children going missing is [increasing]. The term 'kidnapping' is broad. The problem is the reason for a child's disappearance is only known once the kid is found. Those behind kidnappings are usually opportunistic criminals."
A source in the FCS unit said there was "serious cause for concern" at how investigations were conducted.
"The police don't have a handle on this. There are provinces where the situation is completely out of control, such as in Mpumalanga, where younger and younger children are being kidnapped," said the source.
"The situation around missing children for the entire country is dire. Police officers have no clue on... the need for speed in locating children."
Mpumalanga police spokesperson Brig Leonard Hlathi said that since November eight out of 13 kidnapped children had been found murdered.
Two were children with albinism, who were believed to have been killed for muti. The other six were raped before being killed.
"This is just too much. We cannot hide from this. We are not even talking about the others who we have not found," he said.
In the Western Cape, detectives are investigating a "disturbing pattern" of crimes against children in Cape Town.
At least three girls have been snatched near schools in Zonnebloem and Steenberg, and some are reported to have been sexually abused before being set free.
The Western Cape education department received at least two further reports in the past two weeks of attempted abductions, according to spokesperson Jessica Shelver. Most of the abductions are happening in daylight and in public spaces.
Western Cape police spokesperson Lt-Col André Traut said police stations had been directed to "intensify their crime-awareness efforts".
He said: "Provincially, a detective task team looking into crimes against children [rape, abduction and murder] has been set up. Scheduled regular engagements with the Hawks, who investigate child and human-trafficking cases, take place in an effort to share and consolidate information."..