Kids from five schools in the northern rural province of Limpopo suffered diarrhoea, dizziness, vomiting and cramps after eating contaminated beans supplied through a government scheme for feeding the poor.
The primary and secondary school children were admitted to hospitals and local clinics, but most have now been treated and discharged.
Spokesman Elijah Mhlanga said the Department of Basic Education was considering "laying criminal charges" against two companies whose services have now been cancelled.
Thousands of South African children from impoverished households rely on the feeding scheme for nutritious meals.
The department of education promised to introduce stricter monitoring measures to ensure the safety of food.