Emergency crews rushed to Maddox Road in Newport around 2.45pm on Monday afternoon after the youngster was discovered unresponsive in the vehicle by one of his parents.
The youngster was found "unresponsive" by his mother about 2.45pm on Monday as the temperature soared to more than 30C.
He remains in a serious condition at the Royal Children's Hospital where his family holds a vigil at his bedside.
The mother had dropped the boy and his siblings off at St Margaret Mary's Catholic Primary School in Melbourne yesterday morning, police said.
Unaware her son was in the auto, the woman continued on for 10 minutes to her workplace at another school in nearby Newport, at Maddox Road.
The boy was taken to hospital where he remains in a critical condition.
It has been confirmed that he is the son of a staff member at the nearby Newport Gardens Primary School.
Homicide Squad detectives have been notified about the incident, "as per protocol", Victorian police said.
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'The incident didn't involve any students from our school, ' he said.
'Support will be made available for any staff, students and families that need it, ' Mr McGlade said, asking for privacy for those involved.
It was approximately 32C in Melbourne yesterday, and the temperature inside a hot vehicle is nearly double that of outside.
"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.
One resident told the Herald Sun: "It's just a very sad situation".
"I can't imagine what the parents would be going through".
Maddox Road has been blocked off by police.