The National Professional Teachers' Organisation of South Africa in Eastern Cape has called on its members to return to school.
Naptosa provincial boss Peter Duminy said the civil servants' strike was over for its members.
Duminy encouraged his members to report any incidents of intimidation.
"They won't be escorted by the police or soldiers," he said.
Sowetan visited former Model C schools in the East London area where most staff are Naptosa members.
Principals and teachers at the schools were not willing to talk.
Unlike state schools in the province, pupils at some former Model C schools had written their mid-year examinations.
Teachers, who wanted to remain anonymous, said some schools had written examinations and it had been business as usual.
"Only a few pupils attended school yesterday because our pupils have already completed exams," said one teacher.
Provincial Education Department spokesman Loyiso Pulumani said former Model C schools were conducting classes, but most schools were still closed. He said there was a slight improvement in attendance yesterday with more than 50percent of staff back at work.
Pulumani said: "Sixteen out of 23 districts were contacted. Ten district offices reported that less than 50percent of employees were at work. Six district offices reported that more than 50 percent of employees were back at work."