The department launched an investigation after pupils in Sekhukhune, Limpopo, were hospitalised after consuming food from the programme last month, the Sowetan reported on Tuesday.
On September 25, two pupils found pieces of glass and small stones in the beans they were eating.
“The school reported the matter to the department of health, who took 238 pupils to Jane Furse and St Rita’s hospitals for medical check-ups,” the report said.
It found that every bag of beans opened in different schools contained small stones and pieces of glass.
The report advised schools not to cook the beans.
The multi-million feeding scheme funded by government distributes beans and fish to schools in impoverished areas.
Last week, pupils at Ntaki Primary School, also in Sekhukune, complained about a similar problem.
Pupils reportedly vomited blood after eating food at school and were taken to hospital.
The department confirmed the incident to the newspaper.