Johannesburg - Schooling in Daveyton, Ekurhuleni, was disrupted on Wednesday following a protest by residents trying to illegally invade land.
"Parents are keeping them from school and some parents are choosing to take them out of school out of concern for their safety," Gauteng education department spokesperson Phumla Sekhonyane said.
No schools had been closed in the area.
Education MEC Panyaza Lesufi said it was of "extreme" concern that when communities engaged in protests, schools became targets resulting in pupils losing valuable time.
Lesufi said the department was in the process of engaging the community to prevent further school disruptions.
"At this stage we would like to make an appeal to community leaders to assist the department in stabilising schools in the area and ensure that the future of young learners is not placed in jeopardy," he said.
"We will continue to closely monitor the situation and hope that the community and relevant authorities will speedily resolve the unrest."
The protest in Daveyton began on Monday when residents tried to illegally invade land and erect shacks but were prevented from doing so by authorities.
On Tuesday night, shops owned by foreigners were looted in the area.
Six people were arrested and were expected to appear in the Daveyton Magistrate's Court soon.
Rocks which were used to block roads on Tuesday were removed by Wednesday morning, but some intersections remained blocked, said Ekurhuleni metro spokesperson Wilfred Kgasago.
He said a meeting between protesters and officials was scheduled for Wednesday to try to resolve the issue.
Another meeting was planned for Thursday.