Emergency services were called to the brick home in Sydenham, in Melbourne's north-western suburbs, just after 9.30pm on Sunday to find smoke and flames billowing from its roof.
The children, aged five, three and one, were rushed to the Royal Children's Hospital where they remain in critical conditions.
Detectives are investigating the circumstances of the blaze after the children were found unconscious by firefighters who were unaware anybody was home.
Neighbours reported hearing a loud bang before fire broke out at the suburban brick house. (Con Chronis/AAP PHOTOS)
Detective Acting Inspector Adam Henry said despite claims neighbours had heard a loud bang before the fire, there was no evidence the children, or anyone else, were playing with fireworks.
Investigators believe the fire started inside a room at the rear of the property, he said.
Det Henry confirmed police had spoken briefly to the children's distressed mother, who was with them at the hospital, and would formally speak to her again.
He was unable to clarify if she, or someone else, was at home with her children at the time of the fire.
"At this stage its too early to say whether the fire is suspicious or not and it's important that we don't pre-empt any possible outcomes or make any assumptions," Det Henry said on Monday afternoon.
"This is a incredibly tragic incident and one that would have been very confronting for the first responders, fire fighters in particular - they did an incredible job to locate the children and get them to hospital swiftly."
Police say investigators will be at the scene for a number of days. (Con Chronis/AAP PHOTOS)
Detectives have spoken to people closely related to the family, including a biological father of the children.
The mother and biological father are known to police, he said.
"It's our understanding the family had only moved in a week earlier ... that the mother and the three children lived there," Det Henry said.
"At this point in time, there's no suggestion that a third party was involved."
Thirty firefighters tackled the blaze which was billowing from the roof of the house. (Con Chronis/AAP PHOTOS)
It took 30 firefighters and 10 appliances, including an aerial unit, several hours to extinguish the blaze.
Firefighters located a seemingly uninjured pet dog at the scene on Monday morning.
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