"These babies in dustbins, gutters, dumps...who are aborted or miscarried newborns being disposed of...are becoming a large part of 60% of undetermined deaths (of young children) in Gauteng," Professor Jeanine Vellema told reporters in Johannesburg.
"We find these dumped babies when they are dead and we often cannot find out how they died," she said.
Vellema was a speaker at a presentation on fatal injuries in Gauteng in 2009, an initiative by the MRC and the Unisa, supported by the department of health.
She said the service was aware of an increased number of dumped babies in certain areas, particularly in urban, metro areas of Johannesburg.
"We've also seen an increase towards the northwestern suburbs of Gauteng," she said.
Vellema said it was not clear why these babies were being dumped.
"Is it people who are ill-informed about what to do with a baby or dead baby after birth?"
She said it was important to note that these deaths were not reported, and it was only because of their discovery by others that their numbers were known.
Abortions were the leading external cause of death in 2009 for children aged 0 to 4, where a cause of death was known, the MRC presentation revealed on Thursday.