A staff member is accused of assaulting the girl, who is understood to be intellectually impaired, at the home west of Brisbane.
Queensland's Child Safety Minister Amanda Camm confirmed the alleged attack was being investigated, saying she had zero tolerance for abuse "particularly when it comes to vulnerable children in care".
"Queenslanders would rightly expect that anyone convicted of such a heinous offence deserves to face the full force of the law," she told reporters on Wednesday.
Detectives are investigating the alleged August 20 assault at the home operated by Lighthouse Child and Family Services.
The Queensland out-of-home residential care provider for vulnerable children and young people has been contacted for comment.
The allegations have been raised as pressure mounts on Ms Camm after the Liberal National government claimed it had inherited a "broken" child safety system, sparking a rebuild.
Ms Camm said a Commission of Inquiry found around 67 per cent of reported sexual exploitation in state care involved children in residential care.
"Sixty-seven per cent of children in residential care that have reported sexual abuse allegations is unacceptable," she said, adding the government did "not have a moment to waste" in reforming the system.
Ms Camm said contracts had been cancelled where residential care providers failed to meet safety and quality standards, and that such providers "have no place" in the system.
Acting Deputy Commissioner Rhys Wildman confirmed the residential care allegation was under active investigation.
But he declined to provide further detail, citing the victim's vulnerability.
The alleged rape comes as the Queensland government look to establish an agency aimed at improving the protection of children from sexual abuse.
Attorney-General Deb Frecklington said the Queensland Protection Commission Bill would be introduced to parliament on Wednesday.
The legislation will help set up the Queensland Protection Commission, expected to start in early 2027.
The commission would be a "nation-leading" safeguarding agency for children and vulnerable people, bringing key child protection checks and safeguards under one roof, Ms Frecklington said.
"It is vitally important that we set up an agency ... so we can push back on predators to make sure that Queensland children are kept very safe."
The commission was set to be be launched with $255 million across the next four financial years.
It was set up after a Child Death Review Board report found there were multiple opportunities missed to stop one of Australia's most notorious paedophiles, Ashley Paul Griffith.
The state government also responded to 52 recommendations made in a Child Safety Commission of Inquiry final report released in June.
It accepted 32, saying they would be injecting $200 million to implement them within 30 months.
The 11-month inquiry's report exposed years of systemic failure, revealing no child had been adopted from state care since 2019.
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