"The boy's mother dropped her children at primary school in the morning however didn't realise one of the kids had climbed into the rear of the auto and hid himself", police said in a statement.
Authorities were called to Maddox Road in Newport just after 2.45pm after an "incident" involving a child.
Police focus on a black Kia Carnival van.
The young boy who is now clinging to life in hospital was found in the family Kia Carnival on Maddox Road in Newport, Melbourne, at around 2.45pm on Monday and had spent several hours inside the auto.
Police, firefighters and paramedics rushed to Maddox Rd in Newport around 2.40pm, after reports of a child trapped in a vehicle.
More than 24 hours later, the boy remains in a serious condition at the city's Royal Children's Hospital, The Australian Herald reported.
'She has driven to work and parked her auto without knowing he was in there'.
Police said they are treating the incident as an accident.
The vehicle is taken away on a tow truck.
The school is located about 100 metres from where the boy was found.
Catholic Education Melbourne, which runs St Margaret Mary's, is offering counselling to all children and families affected by the incident.
The boy's school is less than four kilometres from where he was discovered in the vehicle.
A boy who was found unresponsive in a auto in Newport on Monday had been hiding in the rear, police have revealed.
His classmates and teachers are being offered counselling and support.
'It is unclear at this time how the boy came to be in the auto however the incident is not believed to be suspicious at this time, ' Sen-Constable Thomson said.
While the day started as normal for the family, the boy never made it to school.
Even on milder days, temperatures inside a auto can exceed 50 degrees in as little as 20 minutes, putting anyone inside at great risk for heat stroke, which can lead to a high fever, dehydration, seizures, stroke and death.
In summer, it can be up to 30C hotter than outside.