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No disruptions were reported in schools across the country as pupils returned to classes yesterday, except for Khutsong.
North West's education department said that a teacher was intimidated and tyres burnt at one of the high schools.
Education department spokesman Charles Raseala said no one was injured, but classes had to be adjourned for the day at Badirile High School.
"Apart from this incident no disruptions were brought to our attention. About 99percent of teachers came to school while the number of pupils who turned out was low," he said.
"We can obviously attribute the poor attendance to the recent disruptions in Khutsong. I guess parents and pupils were not sure what would happen. But we are optimistic that more pupils will come to school as the week progresses," he said.
Schools in Khutsong have been closed for the past three months as teachers and pupils boycotted classes as part of the protest by residents against the incorporation of Merafong municipality into North West.
In Gauteng pupils also trickled to school while teachers turned up in their masses to make up for lost time.
On Friday, Education MEC Angie Motshekga met with teacher unions to discuss intensifying the recovery plan in Gauteng.
The recovery plan was started on July 2 to lessen the impact of the recent strike on pupil performance.
Western Cape schools got off to a smooth start.
Education MEC Cameron Dugmore said: "I am pleased with reports that the third term has started smoothly, with good attendance by teachers and pupils.
"This morning it was back to normal for all our 96000 pupils in high and primary schools. Though schools have been affected differently by the recent public service strike, I am most concerned about matrics who have not written exams at all at about 50 high schools," he said.
"These schools must start examinations soon, so they can be completed by August 8. Schools writing their own papers must submit comprehensive examination plans and their timetables by Friday," he said.