Two of three children who were found unconscious in their burning home in Melbourne have tragically died in hospital.

Police confirmed the sisters, aged five and one, had died surrounded by family on Wednesday morning.

The third child, three-year-old boy Kalais, remains in a critical condition in hospital.

The children were discovered inside the Sydenham house, in Melbourne’s north-west, when emergency services rushed to the brick property on Sunday night.

Smoke and flames billowed from the roof while the children were inside. It took fire crews about half an hour to retrieve them.

The young siblings were transported with critical injuries to the Royal Children’s Hospital.

Detectives from the arson and explosives squad are investigating the fire amid questions over whether the children had been left alone.

Police are also investigating who was in the property at the time and just before the blaze.

It’s understood the mother had only recently moved into the property with the children.

The surviving boy’s father, Jayde Petalas, told the Seven Network on Wednesday his son’s condition had improved and doctors were planning to remove his breathing tube.

Petalas, who did not live at the property, described his son and stepdaughters as “happy little kids”.

“They would have been petrified. I hope they didn’t feel anything to be honest,” he said.

“Obviously they would have, but I just tell myself they didn’t.

“It shouldn’t have happened.”

He appealed for help to care for his son on GoFundMe.

“I don’t think the road to recovery is doable on my own as a single father aged 27 to the expectations he deserves after everything we have been [through],” he wrote.

“Any and every little bit of help would mean the world to us and get that little bit closer to getting [our] lives back to somewhat normal thank you so much.

-with AAP