A special needs education assistant at a prestigious Perth private school has told how a senior psychologist was "wide-eyed" and "seemed a bit out of control" after she saw her throw a cup of water in a 12-year-old autistic boy's face.

Agni Angelkovska, 50, is on trial in the Perth Magistrate's Court accused of twice assaulting the student during an incident at Christ Church Grammar School in Claremont in November 2014.

Prosecutors allege Dr Angelkovska hit the boy in the face with his own hand and threw a cup of water at him after he had a "meltdown" at the school and the pair were in a sensory room in a special needs unit.

Testifying today, education and special needs assistant Sally Nelson said she helped three staff members carry the boy, whom The West Australian has chosen not to name, to the special needs unit and helped calm him by applying a blanket and pressure as he lay on the floor.

Camera Icon Sally Nelson. Credit: Simon Santi / The West Australian

The court was earlier told the boy had started throwing witches hats and kicking a motorcycle after he was told he could not take the bus to sport because of an earlier incident.

Ms Nelson said she left the room for about half-an-hour and returned to hear Dr Angelkovska in the curtained sensory room with the boy and stationary strewn across the floor.

She said she could not see behind the curtains but heard "the sound of slapping" and Dr Angelkovska, who headed special needs services and uses the first-name Anne, saying "do you like that?"

The witness said a short time later, teacher Lisa Venn handed Dr Angelkovska a glass of water before the accused woman threw it at the alleged victim’s face and upper chest.

"(The boy) was pretty shaken and shocked by what happened," Ms Nelson said.

"Anne seemed to be quite wide-eyed, heightened I guess."

When Dr Angelkovska's lawyer Simon Freitag suggested his client drank the water and handed it back to Ms Venn, Ms Nelson said: "No, that's not what happened".

Asked what she meant by the word "heightened", Ms Nelson said Dr Angelkovska's "eyes were very large and wide open and she seemed a bit out of control to me".

The boy's mother broke down tears during the testimony of education consultant Michelle Bishop, when she said she was "disturbed" after a meeting with Dr Angelkovska five days after the alleged incident.

Ms Bishop, who was employed with the Association of Independent Schools of WA, said Dr Angelkovska contacted her on advice from the school's headmaster for advice on whether her "behaviour was appropriate".

Camera Icon Education consultant Michelle Bishop. Credit: Simon Santi / The West Australian

She testified that in a face-to-face meeting, Dr Angelkovska "told me she was trying to teach the consequences for his behaviour".

"She said that he'd had a history of difficult behaviour and he needed to learn if you smack somebody, they are going to smack him back," she said.

Ms Bishop said Dr Angelkovska admitted smacking the boy and "said he'd thrown things ... so she threw back".

Asked by prosecutor Cillian Stockdale about whether she had a "clear recollection" of the meeting, Ms Bishop said she did.

"I was quite disturbed after that conversation, that that incident had happened, that that student was treated that way" she said.

Under cross-examination, Ms Bishop admitted the alleged admission was not contained in an email to the headmaster and her first police statement, and that she spoke to the prosecution about the conversation for the first time last night.

Ms Bishop later said she did tell the headmaster over the phone and said “I was well aware he already knew what had happened, it was in the incident report”.

She rejected Mr Freitag’s suggestion that her recollection of the incident was “unreliable”.

“I think when a student is physically harmed … that’s something I would not forget,” she said.

Dr Angelkovska, who has pleaded not guilty to two counts of common assault, claims the boy hit himself accidentally during a struggle and denies throwing water.

The trial continues.