One of the recommendations highlighted that schools now have the rights under federal law to discriminate against LGBT students.
A review of religious freedoms included a recommendation to allow religious schools to discriminate against students on the basis of their sexuality.
"These laws are no longer appropriate, if indeed they ever were appropriate".
"Our Government does not support expulsion of students from religious non-State schools on the basis of their sexuality", Mr Morrison said.
"I believe we can use this goodwill to go further and remove the exemption that would allow a teacher or school staff member to be sacked or refused employment due to their sexual orientation", he said.
But Mr Morrison revealed on Saturday the coalition would reject the advice, opting instead to strengthen discrimination laws to make sure no school can discriminate against LGBT young people. Dave Sharma, Liberal candidate for Wentworth, also said he believed independent schools should "absolutely not" have the right to discriminate against gay teachers.
The school bill is expected to sail through parliament with the support of the main opposition Labor Party.
On Thursday night the Prime Minister appeared on The Bolt Report on Sky News and stated that the government did not support gay kids being expelled.
Australian Prime Minister Scott Morrison speaks during a news conference at Parliament House in Canberra, Australia, September 19, 2018.
"I would not like to see that used as a wedge to get rid of the immediate issue to ensure our children aren't subject to discrimination", Moses said.
"What I'm most concerned about now is that children are at risk of being expelled from schools", he said.
Spokesperson for just.equal, Rodney Croome, said that preventing discrimination across school communities would be in the best interests of children. Morrison said the taks would be undertaken within the next fortnight and "will give all students and parents the certainty they require".
"Given recent misreporting, we have an opportunity here to bring forward a simple amendment to end the confusion".
The Government has been sitting on the Ruddock review, which was set up in the wake of last year's vote on same-sex marriage, since May.
At the time, the Sydney Morning Herald reported that Morrison had defended the report, saying: "We're not proposing to change that law to take away that existing arrangement that exists".