Thomas Hlongwane, president of Sapa in Gauteng, said members at high schools felt the vacation classes should go ahead "because township pupils need all the contact time they can get".
He added: "My personal view was that as the infection rate was going up in Gauteng it wouldn't be prudent to have learners attending. But it was the view of the collective that classes should go ahead."
Moloko Matsapola, principal of Dendron Secondary School, one of Limpopo's top-performing schools, said 207 matrics would have vacation classes in 10 classrooms.
"We are struggling a lot this year because we have to try and close the gap for 2020," Matsapola said.
Hennie Pieterse, principal of Rustenburg High School in North West, said extra classes for the 255 matrics were "too risky".
Dawie Kriel, principal of Noordheuwel High School in Krugersdorp, Gauteng, said holiday classes had been postponed until October because of an outbreak of Covid cases at the school.
Limpopo education department spokesperson Tidimalo Chuene said classes will go ahead in all but two districts, and the Western Cape education department said holiday classes at 160 schools will either be face to face or live-streamed.
Northern Cape education spokesperson Geoffrey van der Merwe said the classes will target 10,344 matrics at 98 underperforming schools. In Mpumalanga, classes will be held for 194 schools that achieved a pass rate of below 70% in last year's matric exams.