The vehicle had been parked outside Hambledon State School in Edmonton, Cairns.
Goodstart's CEO Julia Davison said it had temporarily suspended pick-up and drop-off services in the wake of yesterday's tragedy.
Appearing on Sunrise, she said: 'All of our 15,000 educators are devastated and shocked.
'It is every family’s worst nightmare that something might happen to their child and it is every educator’s worst nightmare something might happen to a child in their care.'
Ms Davison said they don't yet know how the tragedy occured but confirmed police and other agencies are investigating.
The driver of the bus was taken to hospital suffering from shock and distress after the boy's discovery.
It's thought the child boarded the bus that morning and was due to be dropped off at a day centre not far from the school.
He was found at 3.15pm after temperatures in Cairns soared to 35C.
In a statement issued on Tuesday night, Queensland Police said: 'The boy was located deceased on a minibus parked out the front of a school on Stokes Street.
'Cairns detectives from the Child Protection Investigation Unit are investigating the circumstances surrounding the incident.'