An 18-year-old woman is expected to appear in the Mthatha Magistrates Court on Tuesday on a charge of concealment of birth.
Spokesperson Captain Khaya Tonjeni says the teenager was arrested after an infant was found in a plastic bag hidden inside a toilet on a University Campus.
Police would not divulge the name of the University in order to "protect its image."
Tonjeni says it is alleged that the woman had a misunderstanding with the father of the child which led to her aborting the baby.
He says once the age of the foetus is determined, only then could a possible charge of murder be added.