Eastern Cape MEC for education Johnny Makgato has threatened to declare Embekweni Primary School dysfunctional and to freeze the salaries of all its 22 striking teachers.
Makgato, who met parents for six hours on Thursday, told a meeting at a packed school hall that when a school was not performing, the only option for the authorities was not to pay the staff.
"We will freeze all salaries because there is no teaching taking place at this school."
Makgato said he would inform the province's premier, Nosimo Balindlela, that the school, near East London, was dysfunctional.
Parents booed Makgato when he said a commission of inquiry would be set up to investigate problems between parents and teachers.
Two weeks ago, he listened to the grievances of both sides.
There was anger when Makgato produced a letter by the principal, Pakamile Tyindyi.
He said that the principal wanted to resign, citing his safety as one of the reasons.
Makgato said Tyindyi had mentioned names of people in the letter and this would be treated very seriously.
He noted that the commission would interview Tyindyi, teachers and parents - all of whom had made serious allegations against one another.
"Everybody will have to make a submission and the truth will come out," Makgato said.
He said the commission would be made up of the provincial government's senior legal advisers and officials from the premier's office.
Tyindyi illustrated his frustrations [in the letter] that children came to school everyday and then returned home without being taught anything.
Tyindyi said: "I can't sleep at night because I constantly worry about the children.
"I have developed a habit of sleeping in the afternoon after returning from work. It does not make me happy when I think about the fate of the children," Tyindyi said.
Makgato was forced to listen to angry speaker after angry speaker.
Sizakuyinyova ke ngoku [we are going to cause trouble now], said one angry mother with a chorus of approval from other parents.
Makgato explained that before he received the letter from Tyindyi, he had briefed parents about his decision on the commission.
Education district director Mpangazita Ngwanya assured parents that 15 of the 17 teachers currently boycotting classrooms would be at school today.
Teacher Phumzile Mtatase, who is also the deputy principal, and Thembile Mncotsho, who are at the centre of controversy with the parents, are not expected to return to the school for the time being.
Parents have accused Mtatase and Mncotsho of causing most of the problems at Embekweni Primary School.