Mr Morrison has confirmed that the government would seek to amend the Sex Discrimination Act to ban faith-based schools from expelling gay students, at the same time as it attempted to pass its religious discrimination bill.

The Prime Minister was forced to clarify his position on Friday afternoon after Assistant Minister to the Attorney-General Amanda Stoker had earlier on radio suggested the religious discrimination bill would need to be passed first.

"That is my intention, yes," Mr Morrison said when asked if the Sex Discrimination Act would be amended at the same time as the religious discrimination bill was debated.

Asked if that would happen before the election, Mr Morrison told reporters in Melbourne: "Yes."

The comments came as two parliamentary committees probing the religious discrimination bill handed down their reports on Friday afternoon, with both recommending the contentious legislation be passed subject to a range of amendments.

The committee reports provide the strongest signal yet that Labor won't oppose the bill when it returns to the Federal Parliament next week. The government is in a race against time to pass the laws, promised ahead of the 2019 election, before Australians head to the polls later this year.

Mr Morrison will have to navigate more internal Coalition tensions after committing to finally delivering on his three-year old pledge to ban religious schools from expelling students.

The commitment will appease Liberal moderates such as Katie Allen, whose support for the religious discrimination bill was contingent on protections for gay students.

But it threatens to inflame angst among conservatives in the Coalition and anger religious groups, creating another headache for Mr Morrison on the eve of the federal election.

Mr Morrison's commitment, first signalled on Thursday amid the furore over a Queensland school issuing enrolment contracts requiring students to denounce homosexuality, represents a shift in the government's official position.

While Mr Morrison has been clear faith-based schools shouldn't expel gay students, his government had been awaiting the findings of an Australian Law Reform Commission review before moving to amend the Sex Discrimination Act.

The commission was only due to report back 12 months after the passage of the religious discrimination bill, meaning any changes wouldn't be made until 2023.

A group of Liberal moderates had been pushing for the Sex Discrimination Act to be amended immediately, and believed they had agreement from Attorney-General Michaelia Cash to do so in exchange for their support for the bill.

But Senator Cash appeared to quash any deal when she told an online event hosted by Christian lobby group FamilyVoice in December that the government's position had not changed.

But the government has now pivoted.

In an interview on ABC RN Breakfast on Friday morning, Senator Stoker had suggested the government was looking only at options to "compress" the 12-month timeframe between the passage of the bill and the axing of the school expulsion power.

She warned making changes before the religious discrimination bill was in its "final form" risked creating unintended consequences. The religious discrimination bill is scheduled for debate in the lower house on Tuesday.