The man, named by multiple media outlets as 34-year-old Wayne Godinet, was reportedly trying to rescue his children when he succumbed to the blaze.
The family's 28-year-old mother, identified in reports as Samantha Stephenson, survived the inferno by escaping when the two-storey Russell Island home was engulfed in flames about 6am on Sunday.
Police said a 21-year-old woman also escaped the house unharmed.
Emergency crews arrived to find the two women outside the house suffering smoke inhalation.
Witnesses said Ms Stephenson was seen screaming for help, telling first responders her family was trapped inside the burning home.
The blaze spread to two other properties that were saved by firefighters.
Several people from the neighbouring properties were also treated by ambulance officers for smoke inhalation and minor burns.
Three people were taken to hospitals on the mainland for treatment, including Ms Stephenson.
Authorities spent Sunday afternoon at the scene working to piece together the origin of the fire.
Fire investigators found the bodies of Mr Godinet and the five boys - aged 11, 10, twins aged four and a three-year-old - inside the burnt-out home late on Sunday.
A post-mortem and scientific examination will be conducted to formally confirm their identities.
The small Russell Island community has been hard hit by the tragedy, with the victims known to local emergency personnel.
The eight-kilometre-long island lies between the Queensland mainland and North Stradbroke Island and has a population of about 3700.
Queensland Police Commissioner Katarina Carroll thanked the "brave" first responders for their efforts at what could only be described as a devastating scene.
Queensland Premier Annastacia Palaszczuk and others shared sympathies for those involved in the tragedy.
"My thoughts are with the whole Russell Island community at this very sad and tragic time," she tweeted on Sunday.
Local authorities are setting up a fundraising account through the local registered charitable trust, The Redland Foundation.
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