Child Services Minister Craig Crawford said the abuse, neglect and violence suffered by teens, known by the pseudonyms Kaleb and Jonathon, should never have happened.
Both were found naked in a bedroom with the door handles removed, in soiled nappies and with their dead father in a nearby room in 2020.
A year earlier, one of the boys was witnessed gnawing on a dog bone when a public tip-off prompted a visit by authorities to their Brisbane home.
These details were unearthed at a public hearing of the Disability Royal Commission in May.
"This should never have happened. This should not happen in our country and it should not happen in our state," Mr Crawford told reporters on Tuesday.
The plight of the teens was likened to "torture" by Commissioner John Ryan, with counsel assisting the commission Kate Eastman saying government agencies were aware of risks to the boys.
In its three findings handed down on Tuesday, the report says Kaleb and Jonathon experienced violence, abuse, neglect and the deprivation of their human rights in the care of their father between 2000 and May 2020.
The abuse they suffered was preventable and the government could and should have done more so that Kaleb and Jonathon would not have experienced the deprivation of their human rights, the report says.
Five recommendations have been proposed including an apology and compensation from the government, which should examine whether current policies and practices are sufficient to prevent the extent of human rights being deprived from children with disabilities.
Better training and resources for relevant government departments also form part of the recommendations to address the influence of unconscious and conscious bias, and how discrimination occurs towards children with a disability.
The state should also consider a review of whether or not the mandatory reporting by persons engaged in particular work - a provision of the Child Protection Act - should apply to all Queensland police officers.
Mr Crawford said a recommended independent review of the findings will be considered, as well as compensation.
"We need to allow time as a government to go through the report, to be able to speak with all of those agencies," he said.
"We need a deep dive by various government agencies on this one."
Opposition spokesperson Amanda Camm said the shocking treatment of the two boys will reverberate around the state.
"Today Minister Crawford needs to explain to Queenslanders what will be done to ensure this never happens again," she said.
The final report for the Royal Commission into Violence, Abuse, Neglect and Exploitation of People with Disability is due by September 29.
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