While Grade 7 and Grade 12 pupils have been back at school for a few weeks, the phasing in of the other grades are commencing this week.
However, protesters called for the school year to be suspended in order to keep school staff and children safe.
More than 500 pupils, 1 169 staff members and 775 schools in the country have been affected by Covid-19, according to the Department of Basic Education (DBE)
At least three teachers have died of Covid-19 in the Western Cape.
The DBE has rejected calls to suspend the academic year.
Parents of Seaview Primary in Rocklands, Mitchells Plain, came armed with placards and picketed on Eisleben Road.
Fasheeg Rorick, 32, from Rocklands says he has two children in Grade 1 and Grade R, and fears for their safety.
“We were told that we must sign a form stating that if my child gets infected at school, the school won’t be responsible for it, what nonsense is this?”
Grade 7 teacher David Stephens says: “I think it’s irresponsible of us to have children and teachers at school at the height of the pandemic.
“What about our children who are infected at home and come to school and infect others?
“Parliament is scared to open, so why should schools open?
“We are being held at gunpoint, where they say if you don’t (come to work), you will lose your job.”
Grade 5 educator Dawn Cockrill, 51, says Caradale Primary was closed for decontamination yesterday after a positive case was reported.
“We are concerned about the kids’ emotional well-being, I’ve seen how this affects the Grade 7 pupils, the boys can’t kick ball, we see them filled with fear and anxiety,” she says.
“At first they said we were going to phase it in, but now everyone must come at one time.
“If this is the only option, then give us space, give us substitute teachers.”
Meanwhile in Strand, teachers from Nomzamo Primary, Simanyene High and Christmas Tito Primary used their break time to picket on the nearby N2 highway, calling for the closure of schools as more teachers contracted Covid-19.
Western Cape Education MEC Debbie Schäfer has lashed out at protestors and says disruptions at school are harmful to pupils.
“These organisations claim to have the safety of teachers and learners at heart. However, it is their own actions that are putting our learners’ and teachers’ lives at risk,” she says.
“Video evidence shows people entering schools, and organisations taking learners to the streets, not wearing their masks correctly, nor adhering to physical distancing.”
The SA Democratic Teachers Union has said it supports any action taken by teachers with regards to their safety in schools.