David Thorley denies all the charges brought against him
A learning support assistant broke down in court as she told a jury how she watched a head teacher intimately examine a four-year-old female pupil.
Amelia Stone said she saw David Thorley prise the child's legs open.
Mr Thorley, 56, from Carmarthen denies 19 charges of sex assaults on children in the trial at Swansea Crown Court.
Ms Stone said in the days after the incident she tried to contact Pembrokeshire council but it said there was no record of her call.
The witness said she, together with a teacher, stood in a room near Mr Thorley's office where the examination was carried out.
The girl had complained of feeling sore, she explained.
She said Mr Thorley took the child's trousers off before beginning the examination.
"I nearly said I'm not happy with what you're doing. If that had happened now I would have done that," she said.
She said at the end of the examination the child asked her: "Miss Amelia, have I been naughty?"
"I felt crushed, this has gone against everything I stood by," she added.
Ms Stone said that in the days after the incident she had tried to contact Pembrokeshire council to talk about a child protection issue.
She said she spoke to someone "who didn't know what they were talking about."
She said she left her name and number, but not the name of the school. No-one, she said, called her back.
A few days later Ms Stone told the jury she was called into Mr Thorley's office.
She said he told her that it was his role as head teacher to decide whether to refer children and families to social services and that the examination had been in response to that.
She described the meeting as "very intimidating."
Ms Stone, who no longer works at the school, claimed everyone was scared of Mr Thorley.
Under cross examination she was told Pembrokeshire Council had no record of her call.
It was put to her that there was a personality clash between her and the class teacher who was the same age.
The trial continues.