Scott Morrison has said that schools should not be able to expel students based on their sexuality, just hours after arguing schools should be run consistent with their religious principles and “no one” is suggesting their right to discriminate should be repealed.

Morrison told Sky News on Thursday that he’ll “happily take the criticism” that he should have ruled out discrimination based on sexuality sooner but claimed the Ruddock religious freedom report had been misrepresented.

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The Ruddock review recommended the commonwealth amend the federal Sex Discrimination Act to provide “that religious schools may discriminate in relation to students on the basis of sexual orientation, gender identity or relationship status”. This positive right would replace existing religious exemptions in federal law that allow discrimination but do not override state laws.

LGBTI advocates fear the effect of the recommendation could be to override state discrimination laws that provide more protection for students – including in Queensland and Tasmania – and Phillip Ruddock himself has not ruled out a federal takeover.

But the government has focused on the report’s proposed safeguards including that schools must “regard to the best interests of the child as the primary consideration in its conduct” and a requirement to publicise a school policy on discrimination, arguing these would limit not extend religious schools’ ability to discriminate.

Morrison told Sky News he was “not comfortable” with schools turning away gay children but accused Fairfax Media – which first reported the Ruddock recommendation – of misrepresenting the report.

Morrison said the Ruddock review was focused on “what is necessary to ensure a positive right of freedom of religion but at the same time not to disrespect or disenfranchise the rights of other Australians” including on the grounds of sexuality.

“I don’t think if someone’s at a school they should be kicked out because they have a different sexuality to what might be believed to be the appropriate thing by a particular religious group.

“We do not think that children should be discriminated against.”

Earlier on Thursday, Morrison told 3AW that “religious schools should be able to run their schools based on their religious principles” and claimed that “no one” is calling for existing exemptions to be repealed.

The comments leave Morrison in the precarious position of having stated a principled opposition to religious schools discriminating on the grounds of sexuality while backing a call to enshrine a right to do just that in federal law, albeit with safeguards.

The Greens have announced they will introduce a bill to abolish the religious exemption to discrimination law, while crossbenchers Derryn Hinch and Centre Alliance’s Rex Patrick have also expressed opposition to the ability to discriminate.

The attorney general Christian Porter has said that the current balance of rights “probably could do with a little bit of fine tuning, but I don’t think that, and it’s not recommended, that the balance be shifted further towards schools being able to discriminate”.

On Friday Labor deputy leader and education spokeswoman Tanya Plibersek said it was “wrong and irresponsible” for schools to turn away gay students and “frankly abhorrent to send that message to a child that something is wrong with them”.

Plibersek told reporters in Sydney the “vast majority” of schools don’t use their exemptions to discrimination law to sack gay teachers or expel gay students, but confirmed it is “not Labor’s plan to reduce any of the existing exemptions”, as she said in January. Labor has ruled out expanding discrimination law exemptions.

On Friday the former international development minister, Concetta Fierravanti-Wells, a leading Liberal conservative, called for the Ruddock report to be released “as soon as possible, so that we can progress to ensuring that the religious freedoms of Australians are protected”.

Fierravanti-Wells joins former high court judge Michael Kirby and the independent candidate Kerryn Phelps, who have both called for the report to be released before the 20 October Wentworth byelection.

Morrison has said the Ruddock review recommendations have not gone to cabinet and the government’s timetable is “to deal with this by the end of the year”, confirming it will not be public before the byelection.