Teachers, parents and provincial education departments this week admitted that lessons for grade 7 and 12 pupils were being severely disrupted.
This comes in the wake of protests on Thursday by teachers from several Cape Town schools, who demanded schools be closed to protect teachers and pupils' lives.
The Western Cape education department confirmed that 236 schools reported having infected staff members. In Gauteng, 176 schools have been affected, with 188 teachers and 58 pupils testing positive. In the Eastern Cape, 132 schools remain shut. Six schools in the Northern Cape and 14 each in North West and Free State also had to close.
David de Korte, national president of the South African Principals' Association, which represents the heads of 3,000 schools, said: "Every single day grade 12s miss is a day they fall behind. The grade 12 programme hasn't been trimmed in any way, so there's no way those children are going to be in the same position as a child who has had seven periods of lessons a day every day."
Professor Nicky Roberts of the University of Johannesburg said there was agreement in many countries that there should be no high-stakes academic assessments of pupils.
"I think this should be our approach for grades R to 11. And we should keep this on the table as a possible option for some or all of our current grade 12s," Roberts said.
Writing in the Sunday Times today, basic education minister Angie Motshekga says SA's schools "offer a new frontier against the pandemic as they are repurposed as epicentres of surveillance, screening, contact tracing and testing of cases that would otherwise have fallen through the cracks".
"We understand the contestation from some quarters as this is a new terrain of struggle, but we shouldn't allow panic to guide public policy," she adds.
"We must be mindful of the reality, as confirmed by research, that the longer marginalised children are out of school, the less likely they are to return."
Motshekga says the current wave of Covid cases reported in schools since June 8 are "classic community transmissions".
"As yet they are not originating from our facilities. However, society must prepare for this eventuality - community transmissions can become bushfires within our schools. It is not a matter of if, but when."