St John ambulance spokesman Ian Henderson said paramedics were called to the corner of Thames Highway and Foyle St at 4.13pm on Tuesday.
He said the boy was transported in a "very serious" condition to Oamaru Hospital, where he was subsequently airlifted to Dunedin Hospital.
The boy was later airlifted to Auckland's Starship hospital, where he remains in an unknown condition.
His condition will be updated this afternoon.
It was understood he had undergone brain surgery.
In a statement from police today, Dunedin Police Detective Senior Sergeant Malcolm Inglis said the incident appeared to be a "tragic accident".
"Police do not believe there to be any suspicious circumstances surrounding the injuries," he said.
"While there appears to be no suspicious circumstances, police are still making some enquiries with a scene examination completed yesterday."
The family were being supported, he said.