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The Morrison government has launched last-minute talks with stakeholders to determine the future of its contentious religious discrimination laws, as advocates call for them to be withdrawn.

The government will seek to overturn amendments to the Sex Discrimination Act, passed against its will, preventing religious schools from expelling transgender students.

Debate on the religious discrimination laws is expected to move to the Senate on Thursday after the bill passed by the lower house in a marathon sitting that ended just before 5am on Thursday.

Five coalition MPs crossed the floor to side with a Labor and crossbench amendment to the Sex Discrimination Act to protect transgender students.

Assistant Attorney-General Amanda Stoker said the coalition was speaking with stakeholders now the package of reforms had been altered.

"We are really intent on honouring commitments we made to multicultural groups and religious groups and LGBTI groups in the consultation process," she told Sky News.

"We're checking in with them, trying to make sure we fully appreciate the implications of that amendment before we have to deal with it in the Senate."

Asked by reporters whether there was a chance nothing would end up passing parliament, she said: "That is, always in a parliamentary process, an option."

Australian Christian Lobby national director of politics Wendy Francis said the bill should be withdrawn due to the changed position.

She told AAP the lobby has been in touch with all government senators.

"The rights of religious schools in this country will be significantly diminished if this passes," she said.

"Taking away protections for Christian schools is a price too high to pay for the passage of the religious discrimination bill."

LGBTQ+ advocacy group Equality Australia has called for the Senate to approve amendments preventing existing anti-discrimination laws from being overridden.

Superannuation Minister Jane Hume said the government would seek to overturn the amendments passed when debate moves to the Senate.

"The government will inevitably move amendments to try and revert the bill back to the government's position," she told reporters.

"When you deal with competing rights, it's always going to be a contentious issue."

Senator Hume said the government still supported a process by the Australian Law Reform Commission to examine the Sex Discrimination Act issues.

Liberal senator Andrew Bragg is likely to cross the floor to side with Labor on the issue of protecting transgender children.

Labor is set to use the Senate to move amendments that were rejected by the lower house.

Independent senator Rex Patrick indicated the contentious bill would not be voted on in the upper house on Thursday.

"The religious discrimination bill will not be dealt with today. It is the Senate that controls what happens in the Senate, not Scott Morrison," he said on Twitter.

The five MPs who crossed the floor of the House of Representatives on the Sex Discrimination Act amendment included Bridget Archer, Trent Zimmerman, Fiona Martin, Dave Sharma and Katie Allen.

Mr Zimmerman said his decision to vote against the government was a matter of conscience.

"(Supporting the amendments) would be a bad signal to send to the transgender community," he told ABC Radio.

"It's hard to cross the floor and people feel passionately about these issues."

Opposition Leader Anthony Albanese said Labor would wait to see how the government pursues the bill in the Senate when debate resumes.

"Their actions after the major amendment was carried were quite extraordinary," he told the Nine Network.

"It isn't too often that governments lose votes on the floor of the House of Representatives, but I've never seen before a government lose votes against a bill they introduced themselves."

© AAP 2022

Debate on the government's contentious religious discrimination bill will move to the upper house after passing through the House of Representatives in a marathon session.

The bill passed just before 5am on Thursday by 90 votes to six after more than 10 hours of debate on the issue, and will move to the upper house later in the day.

However, five coalition MPs crossed the floor to support a Labor and crossbench amendment that would prevent religious schools from discriminating against gay and transgender students.

The Liberal MPs included Bridget Archer, Trent Zimmerman, Fiona Martin, Dave Sharma and Katie Allen.

While other proposed amendments to the bill were voted down in the House of Representatives, Labor has indicated it would pursue them once the bill moves to the Senate.

A long sitting day is expected in the Senate, with Thursday being the last sitting day before the federal budget.

Opposition Leader Anthony Albanese said Labor would wait to see how the government pursues the bill in the Senate when debate resumes.

"Their actions after the major amendment was carried were quite extraordinary," he told the Nine Network on Thursday.

"It isn't too often that governments lose votes on the floor of the House of Representatives, but I've never seen before a government lose votes against a bill they introduced themselves."

Labor also sought an amendment to the controversial statements of belief clause in the bill, but the bill was deadlocked at 62-62, despite two Liberal MPs crossing the floor.

The deadlock was broken by Speaker Andrew Wallace, who voted with the government.

One of the Liberals who crossed the floor, Trent Zimmerman, said his decision to vote against the government was a matter of conscience.

"(Supporting the amendments) would be a bad signal to send to the transgender community," he told ABC Radio.

"It's hard to cross the floor and people feel passionately about these issues."

Shadow attorney-general Mark Dreyfus said Labor was confident the party's proposed amendments would pass the Senate once debate moves to the upper house.

However, he did not say what the party would do if the amendments do not get enough support.

Superannuation Minister Jane Hume said despite members of the government crossing the floor, the coalition wanted to get the balance right on the legislation.

"We don't want to see any children expelled from school ever on the basis of their sexual identity," she told the ABC.

"But at the same time, we want to make sure we respect the rights of parents to choose to send their children to a school that's a single-sex school."

The bill had been referred to the Australian Law Reform Commission to be examined.

Labor MP Stephen Jones said members of the government crossing the floor to support crossbench amendments was a significant move.

"I want to send a nod out to the five Liberal Party MPs who swum against the tide as well and did the right thing," he told the ABC.

"We couldn't have one law changed without the other law being improved to protect transgender, gay young people."

Ahead of the bill's introduction in the Senate, the Australian Christian Lobby has called on the government to withdraw it from the upper house.

The lobby's national director of politics Wendy Francis said the bills now do more harm than good.

"Taking away protections for Christian schools is a price too high to pay for the passage of the religious discrimination bill," she said.

"With the amendments so damaging to religious freedom, the government should immediately withdraw the bills."

LGBTQ+ advocacy group Equality Australia has now called for the Senate to approve amendments preventing existing anti-discrimination laws being overridden.

© AAP 2022

The coalition government's religious freedom laws have passed the first legislative hurdle after Labor secured changes before backing the bill in the lower house.

The religious discrimination bill passed in the early hours of Thursday morning by 90 votes to six, following a mammoth debate in the House of Representatives which heard objections by Liberal moderates and amendment proposals by independent MPs.

But in a blow to the federal government, the opposition and crossbench was ultimately successful in amending a controversial clause of the Sex Discrimination Act allowing religious schools to discriminate on grounds including sexuality and gender identity.

The amendments will prohibit vilification of and discrimination against children based on sexuality and gender identity.

Labor Leader Anthony Albanese said a major issue had been addressed.

"And that is a very, very good thing," he told the Nine Network on Thursday morning.

"We're claiming credit for the amendments that were carried. We fought very hard."

Mr Albanese said Labor wants further amendments to the bill and "we will pursue those in the Senate."

Liberal MPs Trent Zimmerman, Bridget Archer, Fiona Martin, Katie Allen and Dave Sharma voted against the government to amend the bill, with the vote landing 65-59.

Mr Zimmerman had earlier said he would not stand by and make life for transgender people more difficult.

Labor also proposed amendments to ensure a key pillar of the laws - a "statement of belief" clause designed by the government to shield people expressing religious beliefs even if they're offensive - did not override existing discrimination protections.

But the government did not agree.

"We support people's right to practise their faith free from discrimination," Mr Albanese said.

"But this should not remove protections that already exist to protect against other forms of discrimination."

Prime Minister Scott Morrison had on Wednesday he "earnestly hoped" the bill would unite the parliament.

"Let me be very clear tonight - with the bill and the position taken by the government - that we reach out with nothing other than love, care, compassion and support to every child regardless of their sexual orientation or their gender identity," he said.

The government made some small amendments that Labor agreed to, including that - other than the statement of belief clause - the bill will not override existing laws.

Mr Zimmerman and Ms Archer voted with Labor because the government would not agree to amend the bill to clarify the statement of belief clause.

With the statement of belief amendment vote tied at 62-62, Speaker Andrew Wallace's intervention meant the vote was lost.

Ms Archer also voted with Labor after the government did not amend the bill to outlaw vilification of people of faith.

Labor frontbencher Tony Burke questioned what the debate had been about if the government did not want legal protection against people being harassed, intimidated, threatened or vilified because of their faith.

He said the bill - without the amendment to prohibit vilification - did not match what the prime minister had said it was about.

Communications Minister Paul Fletcher said the government does not condone vilification or hate speech but Labor's anti-vilification proposal was "complex" and required careful consideration to balance competing rights.

He said the proposed provisions would create further inconsistencies and confusion between Commonwealth, state and territory laws.

The coalition party room earlier this week agreed to amendments to add a clause to the Sex Discrimination Act prohibiting the expulsion of students because of their sexuality.

But it refused to extend the same protections to transgender children.

Liberal MP Angie Bell, who previously had problems with the bill, backed the legislation in the end because it represented a "net gain for gay rights".

Equality Australia, which represents LGBTIQ+ Australians, called on the Senate to now do its job.

"The responsibility now sits with the Senate to ensure the Religious Discrimination Bill does not take us backwards and to ensure that the amendments to the Sex Discrimination Act that protect students are passed," CEO Anna Brown said on Thursday.

© AAP 2022