The manager of a Cairns childcare center told authorities “my whole life is over” after finding the body of a toddler in the back of the kindy bus he had been driving.

Center manager and bus driver Michael Glen Lewis and childcare worker Dionne Beatrice Grills faced Cairns magistrates court on Tuesday charged with the manslaughter of the three-year-old.

Lewis made a call to triple-zero after finding the boy dead on the Goodstart Early Learning Centre bus last Tuesday afternoon, media reported.

In the call, which was played to the court, Lewis could be heard telling the emergency operator: “Oh my God, this kid is dead.

“The child was left on the bus all day. So sorry, buddy.

“I’m going to jail. Oh my God, my whole life is over.”

Police allege the boy was left on the bus when it was parked for the day outside Hambledon State School, about 1.7km from Goodstart’s Edmonton center, which Lewis managed.

Lewis, 45, was driving the minibus that collected the child from his home about 9 am that morning. The manager found the boy’s body inside the baking vehicle when he returned to it at 3.15 pm that day.

The court was told the boy was a victim of a criminal act of negligence, it was reported.

Grills, 34, was also on the bus on the morning of the boy’s death. She was a casual employee who had been working at the center for less than a month, the court was told.

Earlier on Tuesday, acting detective inspector Jason Smith spoke to reporters outside the court, saying the charges should provide answers for the boy’s devastated family.

“The manslaughter charge refers to an act or a mission which is negligent and has brought about the death of another person,” he said.

“The family is suitably distressed and very upset about this. And hopefully, now that the matter is before the court, they’ll get the answers that they need.”

The close family of the three-year-old boy who died in a daycare minibus leave the Cairns courthouse on Tuesday. Photograph: Brian Cassey/AAP

Goodstart has formally stood aside from the two workers. It’s pick-up and drop-off services remain suspended nationally, and its Edmonton center is closed.

One of the boy’s relatives, Sydney man Thomas Namok, has told the ABC he’s struggling to comprehend what happened.

“We’re all distraught at the moment. We just can’t believe this has happened. We just want answers,” he said.

“He was just a cheerful little boy we would always laugh every time he’s around. That’s what I remember of him. It’s going to be sad he’s not going to be around anymore.”