ER24 paramedics said they reported to the school on Tuesday after receiving reports that the pupils were nauseous and vomiting.
When the children got to hospital, however, it was found that only eight of them needed treatment.
"All the children were thoroughly examined by physicians and declared healthy and bug-free, with no traces of food poisoning," said the school.
"However, eight of the 46 appeared to suffer from stomach ailments but were treated and released with the rest of the children."
Northern Academy, an independent school that also offers boarding facilities, said it wanted to ensure the public that it prioritised the safety of its learners.
It wasn't food poisoning, says Limpopo school after 46 kids sent to hospital
The Limpopo primary school where 46 children had to be hospitalised on Tuesday after complaining of severe stomach cramps has denied that it was a case of food poisoning.
In a statement released on Wednesday, Northern Academy Independent School in Polokwane said the children could have been affected by a bug doing the rounds.
"The area of Polokwane has unfortunately been badly affected by a stomach bug since the start of winter," said the school.
"Medical services were called to inspect and treated the affected children on site. A decision was made to take the children to surrounding medical facilities for proper diagnosis and treatment."
ER24 paramedics said they reported to the school on Tuesday after receiving reports that the pupils were nauseous and vomiting.
When the children got to hospital, however, it was found that only eight of them needed treatment.
"All the children were thoroughly examined by physicians and declared healthy and bug-free, with no traces of food poisoning," said the school.
"However, eight of the 46 appeared to suffer from stomach ailments but were treated and released with the rest of the children."
Northern Academy, an independent school that also offers boarding facilities, said it wanted to ensure the public that it prioritised the safety of its learners.