UPDATE 11/02 - The federal government has decided to push for a Senate inquiry into key parts of its religious discrimination bills; avoiding a vote in the upper house.

Attorney-General Michaelia Cash says she is seeking a Senate inquiry rather than an immediate vote based on legal advice from the Australian Government Solicitor.

She says she had been advised that amendments passed in the Parliament on Thursday morning had “unintended consequences” that could harm students.

ORIGINAL 10/02 - A bill allowing religious discrimination has passed the House of Representatives. 

After a marathon debate, the government's contentious religious discrimination bill passed through parliament's lower house overnight. 

The Morrison Government says its religious discrimination legislation is designed to to stop someone from being discriminated against because of their religious beliefs. However, critics say it allows words and actions that would otherwise be deemed discriminatory to be carried out under the cover of religious belief.

The bill passed the House of Representatives with Labor's support, but five Liberal MPs crossed the floor to vote with Labor in support of a crossbench amendment to create stronger protections for transgender students.

Labor attempted to pass amendments to prevent discriminatory statements in the name of religion, but failed. 

The bill will now proceed to the Senate, where the government will be forced to respond to a call for amendments to the Sex Discrimination Act to prtoect the LGBTQIA+ community.

Labor leader Anthony Albanese, told reporters after the session that his party could not simply vote against the bill on the basis of its objections.

“I'm very proud of what we've managed to achieve,” Mr Albanese said.

“And those people who argued that we should just vote no and not participate also ignored the fact that the issue of discrimination against people on the basis of their faith is real and it is something that Labor supports action on, just like we support removing discrimination on the basis of age, on the basis of gender, on the basis of disability.

“The amendment carried will prohibit schools discriminating on the basis of sexual orientation, gender identity, relationship, or marital status. That makes an enormous difference.”

Equality Australia CEO Anna Brown said she ad a mixed reaction to the outcome.

“Truly mixed emotions as five Liberal MPs cross the floor and vote with Greens, Labor and Crossbench to protect LGBTQ+ students, but only after the Religious Discrimination Bill passed with dangerous provisions intact. In the Senate we will keep fighting for laws that protect us all, equally,” Ms Brown said on Twitter. 

Just.Equal Australia spokesperson, Rodney Croome, said even with amendments, the bill could override state laws that protect the LGBTQIA+ community.

“We will never accept a deal that gives rights to one part of our community but actively takes them from another,” Mr Croome said in a statement.

“The amendment trying to protect LGBTIQ+ students does not go far enough because it does not remove the ability of schools to discriminate under cover of ‘religious belief’, as Citipointe College attempted.”

“Meanwhile, the Government and Labor have agreed not to extend discrimination protections to teachers in faith-based schools, and have worked together to take these protections away from teachers and other staff where they already exist in Tasmania, Victoria, the ACT and Queensland,” he said.