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Beryl Thompson, 53, was ordered to carry out 160 hours' community punishment after admitting nine charges of common assault on four pupils.
She admitted striking a little girl who was in a wheelchair with a pointer stick to the face.
She also admitted holding her cheeks after her teeth had been extracted and lifting her from her wheelchair and off the floor.
She had moved one boy causing a bruise, banged his head on a table and held his head underwater for a couple of seconds during a swimming lesson.
Thompson, who at the time of the offences lived in Kensington Way in Northwich but now resides in Mayfield Drive, Winsford, had denied 14 charges of cruelty while working as a senior teacher at the Dee Banks Special School in Chester.
But her trial at Mold Crown Court came to a halt last week when she admitted nine alternative charges of common assault upon four pupils.
Thompson, a former acting deputy headteacher of the school, was told at that stage that she would not be going to prison.
Judge David Hale told her that, on the evidence, she had been an excellent teacher dealing with extremely difficult and vulnerable children for many years.
But he said there were nine occasions in a 20-month period when she fell below the standards she would have expected from anyone else.
He said: "It fortunately caused no significant injury to any of the children.
"In many of the instances there were no injuries at all.
"I am sure that you are now ashamed at what you have done."
Judge Hale also said he hoped there would not be a council inquiry after witnesses including classroom assistants were criticised in court for not acting sooner.
He said they did not deserve it and he was grateful to them for giving evidence.
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