He suffered a broken leg and deep cuts to his legs and hands.
WorkSafe spokesman Michael Birt said workplaces should not be used for babysitting.
"Taking children to work, particularly where there is a serious risk of danger, is not appropriate," he said.
An ambulance service spokesman said the boy was taken to the Royal Children's Hospital where he was believed to be in a serious but stable condition.
The accident happened at AAA Glass, at Tullamarine, about 2.25pm.
It follows the death early last month of a boy, 12, in a forklift accident at a Braybrook factory that manufactures tennis equipment.
WorkSafe investigators are investigating the latest accident.
The Royal Children's Hospital said the boy had surgery last night.