Two children left home alone have escaped a house fire in Melbourne's north-east which police are treating as suspicious.

A 12-year-old girl and her seven-year-old brother fled a unit in Bamfield Road, Heidelberg Heights when a blaze broke out about 5.30am on Thursday morning.

Metropolitan Fire Brigade spokesman Bruce Weaver said the pair had been home alone.

MFB Sergeant Matt Bull told ABC News the girl had done "a great job".

"She not only saved her life but her brother's life as well," he said.

"She could have just left the unit on her own but she's gone back into the house to get him, so she's done a great job."

ABC News reported that police were concerned the children had been left alone overnight and that officers were questioning the father.

Neighbours said the family had lived at the property for at least six years.

The man was the primary carer of his two children and was described by neighbours as someone who "kept to himself".

Public housing workers were supervising the heavily damaged home being boarded up on Thursday afternoon.

Many belongings such as children's clothes and trophies had been left in the driveway.

Neighbours described the early-morning blaze as "enormous".

A 20-year-old Somali man who lives in a neighbouring unit reportedly woke up to the smell of smoke and found the girl standing outside the burning house suffering from the effects of smoke inhalation.

He called the MFB and brought the two children inside while waiting for emergency services to arrive.

It's believed the girl woke up to find the home full of smoke and rescued her brother before trying to rescue the family dog.

Several neighbours said the fire had started in a heater left on overnight.

Fortunately no adjoining properties sustained any damage.

Victoria Police spokeswoman Kendra Jackson said the fire caused moderate damage to the back of the home and was being treated as suspicious.

Mr Weaver said the RSPCA was called to remove a rottweiler from the property.