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.