Police investigated, but did not prosecute.
In June last year, Pemberton told the Herald on Sunday he had been cleared by the school board, and there was "nothing in" the allegations.
However, the teachers' disciplinary body found differently. It found Pemberton had "manhandled" the Year 4 boy, who was upset and scared by the incident, which he said hurt his neck and throat.
Pemberton was censured for serious misconduct, and his record marked. But the disciplinary committee described the incident as a "one-off misjudgment" in a long unblemished career. Since Pemberton was already retired, it said there was no need to strike him from the teachers' register.
'I had to walk on my tippy toes'
In his account, the boy said he felt choked, and had difficulty breathing when he was grabbed by the collar and pulled out of a row of chairs in the school hall, according to the decision.
The pupils had been preparing to watch a rehearsal of the school play, and the boy described how a girl behind him had been kicking the back of his chair, and continued to do so after he asked her to stop.
When the kicking continued, he turned around to speak to the girl, and blew in her face.
Pemberton, however, believed the boy had spat at the girl, the decision said.
The boy said he "had to walk on tippy toes to avoid being choked" when the teacher pulled him out of the row into the centre aisle. He was then dragged out of the hall, and said he had to "walk quickly to keep up with him" and had to hold his head up high to relieve the force on his throat "as it was hard to breathe".
The girl was also brought out of the hall, and the pair were spoken to about their behaviour.
Pemberton denied the boy's version of events, saying he intervened after he witnessed him spitting at the girl.
He admitted he inadvertently gave the boy "a fright", approaching him from his left, when he was speaking to friends on his right.
He claimed to have turned the boy around to face the front, and so all four legs of his chair were on the ground, placing a hand on his shoulder "so he did not fall off". He then instructed him to follow him out of the hall, where he remonstrated with him.
'No memory' of the incident
In an agreed set of facts, Pemberton said he had no memory of events that occurred immediately after he saw the boy blow in the girl's face. But said: "If I made physical contact with the student, I acknowledge that was a mistake, even if my intentions were to prevent him falling off his chair. There was no need to blindside and surprise him.
"This was an error of judgment. I would never do that again."
However, the boy's version of events was backed up by teacher Caroline Randall, who described seeing Pemberton become "very angry" and red in the face.
"I remember thinking - 'my God, what is he going to do?'," she said.
"He grabbed this boy by the back of the collar, twisted the collar and pulled him to his feet. He then marched this boy to the back of the hall and through the exit door."
She later reported the incident, she said.
The disciplinary tribunal ruled that Pemberton's actions amounted to serious misconduct, despite evidence of his good character and usually calm method of dealing with student misbehaviour.
"Not to put too fine a point on it, [Pemberton's] actions would almost certainly have been commonplace, and even regarded as acceptable, not so very long ago. But times have changed," it said.
It acknowledged that the former principal was not in good health at the time, including suffering from sleep apnoea, which would have impaired his judgment.
It was a one-off misjudgment, and the tribunal was confident that even if he returned to the classroom "there will be no repetition of this type of behaviour".
