The Pentecostal school in Carindale is facing a possible review of its state funding and anti-discrimination action over the contracts sent to parents last week before the start of the school year next Monday.
The pacts said "the college will only enrol the student on the basis of the gender that corresponds to their biological sex" and said homosexuality was "sinful", like bestiality, incest and paedophilia.
The Non-State Schools Accreditation Board is reviewing the contracts, about which complaints have also been lodged with the Queensland Human Rights Commission.
Education Minister Grace Grace, who has a non-binary child, has urged Citipointe to rescind the contracts and protect their students' mental health.
"There is no need to put this additional stress with this hanging over the head of students simply because of their sexual orientation or their gender identity," she told ABC radio on Monday.
"We've had a couple of years of very disruptive schooling with COVID. We certainly don't need this now.
"And we certainly don't need this kind of contract to go out without consultation, is what I understand, on a Friday afternoon before they're due to start their senior online.
"The timing, I think, is very inappropriate. I think this is unacceptable and I call on them to withdraw these contracts as soon as possible."
Citipointe reportedly sought legal advice before issuing the contracts and principal Brian Mulherin insisted that 350 families had been consulted about the contracts over the previous 14 months.
"All these families acknowledged our Christian ethos as the basis for the education of their children," he said in a video statement on Tuesday night.
He said no Citipointe student had been expelled because they were gay or transgender.
The minister said Non-State Schools Accreditation Board chair Lynne Foley had told her the body would try to discuss the contracts on Thursday.
The Queensland Human Rights Commission would also probe complaints made about the contracts, the minister said, and whether they complied with state human rights laws.
Independent Education Union branch secretary Terry White said the contracts attempting to circumvent discrimination laws were "beyond shameful and rejected by our union".
"Practices in faith-based schools, and indeed in any endeavour by faith-based organisations, which is conducted for and funded by the public, should reflect community standards and expectations," Mr Burke said in a statement.
Federal MP Angie Bell said the contracts may be allowed under federal laws, which she said the Morrison government was trying to change.
The Liberal National Party MP said Australia was "not 1950 any more" and Citipointe's contracts were "simply wrong".
"I don't agree with them lumping students, who are unsure about their sexuality or or unsure about their gender identity. I don't agree with them lumping them in with the likes of pedophiles and adulterers," she told ABC radio.
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