Fire crews were called to Old Geelong Road around 9.30pm Sunday following reports of a workplace fire.
When crews arrived, a person was reported missing, the man was found after five minutes of searching.
The man, in his 30s ,was transported to the Alfred Hospital, in a critical condition with upper and lower body injuries.
The fire was contained to the building.
The fire was deemed to have been brought under control within two hours after crews remained on scene during the night.
The cause of the fire will be investigated by fire investigators, but at this point it is not believed to be suspicious.