Isaac Gilchrist, a year 3 student at Muswellbrook South Public School, was on a class trip to Blackbutt Reserve on Tuesday when he was accidentally trapped in the bus' luggage compartment before the drive home. Despite his screams, his absence on the bus went unnoticed until a rest stop near Singleton, more than 30 minutes later.

His mother Nicole Gilchrist said she was furious when she heard about the incident that afternoon.

"It just should never, ever have happened, it's unreal," she said.

"He had been banging and screaming.

"He very easily could have died and that's all I can think about."

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A spokesperson for the NSW Department of Education said a roll-call of the year 3 students was taken as they prepared to board a bus taking them back to Muswellbrook after the excursion.

"After the roll call two students were asked to put their bags in the bus' luggage hold," the spokesperson said.

"At a second headcount, during a rest stop about 30 minutes later, it was found that a student was missing.

"The student was let out of the luggage hold, provided with water, and checked by paramedics on his return to school. He was not harmed."

Ms Gilchrist said the distress of the incident was amplified by the fact Isaac had had recent health concerns.

"He had actually just recovered from a skull fracture and a seizure," she said.

"The school was completely aware of this, he had his own risk assessment done.

"Of all the children for this to happen to it is just unfathomable that it was him.

"He had an operation just five or six weeks ago, he wasn't even back in school full time."

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Ms Gilchrist said she had received an apology from the principal and an offer for counselling at the school, but Isaac would not be returning.

"There was no other option given to me, just that if I did change my mind and he was sent back to that school, then he could get counselling from the school," she said.

The NSW Department of Education spokesperson said appropriate action had been taken involving the staff supervising the excursion.