While gay students will be protected under the amendments from being expelled, the same protections have not been extended to transgender students.
The amendments come after moderate Liberals threatened to cross the floor during debates about how LGBT+ students would be protected under the bill.
Finance Minister Simon Birmingham confirmed the new amendments.
"The proposal that is put forward is to repeal the exemption as it relates to students being exempted from the Sex Discrimination Act on the basis of their sexual orientation. Now it doesn't go further than that," he told ABC Radio on Tuesday.
"It would still be subject to a relatively quick, within 12 months, review by the Australian Law Reform Commission, to try and address the best way to be able to enact any other changes without undermining certain issues around same-sex schools."
The debate will resume on Tuesday when Parliament returns to parliament sitting.
Prime Minister Scott Morrison is confident the bill will pass through parliament.
"I stand by it 100 per cent, and I'm standing with the millions of Australians for whom this is such an important issue," he told reporters in Canberra.
"For many Australians, their faith and religion is their culture; you can't separate them."
However, Morrison has denied religious schools will be able to expel students based on their gender identity.
"This bill does not seek to endorse that arrangement. That's existing law. What we're dealing with today are not those matters," he said.