Investigators have now confirmed that the body of a person, believed to be the sole occupant, has been located in the house.
Crews from Seymour, Hilldene and Bendigo were called to the fire just after 4.30am. It was called under control just after 5.00am.
The cause of the fire is yet to be determined and detectives from the Arson and Explosive Squad remain at the scene.
Operations Officer Charlie Cleary said the small, two-bedroom home had been significantly damaged by the fire.
Further details are available on the Victoria Police website.