Johannesburg - Basic Education Minister Angie Motshekga said she was worried about social issues that were cropping up due to children staying at home for extended periods of time.
The most vulnerable, she said, were faced by a number of social challenges such as violence, unplanned pregnancies, drug abuse and many other social ills.
Millions of South African children of school going age have been home since March due to Covid-19 and some grades were expected to return on Monday.
Some anxious parents, however, have decided not to send their children back amid rising infections rates.
During a briefing on the education department's readiness to welcome pupils back in school on Sunday, the minister said it was of critical importance that young people were kept constructively occupied, engaged and connected through schooling.
Motshekga said she visited a school at an informal settlement on Friday and found that two of the girls in matric had not returned as they were pregnant.
She said they also found that one of the boys had had dropped out.
"In the long run we are going to find ourselves with major social challenges that will have been brought up by the pandemic.
"It is important for all of us as a nation to make sure that indeed we can continue to protect our children, we can continue to engage them even if they're not at school so that they're protected from themselves.
"The risk of them staying too long at homes is ghastly to contemplate," she said.
Motshekgasaid parents who have decided not to send their children back to school over Covid-19 concerns need to follow proper home schooling procedures.
As many parents contemplated the return of their children back to school amid rising infections, Motshekga told them in May that they would not be forced to send them.
She said at the time that resuming schooling was important for learners and saving the academic year.
The entire schooling system could not be held back based on anxious parents, Motshekga said.
However, she said, parents who have decided to keep their children at home needed to apply to Provincial Education Departments for home learning.
"We advise these parents not to go to schools, but rather approach the provincial education departments for help as registration does not take place at school," she said.