"We’ve never needed to protect religious freedom before, but now we do," said author Patrick Parkinson, a professor of law at the University of Sydney and a Freedom for Faith board member.

Essential to the proposed law is the right for church-run organisations - including schools and aged care homes - to hire and fire staff in accordance with their values. That would extend to employees who enter into a same-sex marriage following its legalisation late last year.

"Any religious organisation would want to maintain its moral standards around family life and sexual conduct - at least the right to do so," Professor Parkinson said.

"Christians are not into freedom to discriminate, they’re really into freedom to select."

The submission described that freedom as "an existential issue for faith communities of all kinds", saying if a Christian school cannot select its employees then it "will be indistinguishable from the state school next door", just as Christian health facilities would "quickly lose their character".

The churches have also asked for:

• changes to the Marriage Act to ensure facilities such as school chapels cannot be used for same-sex weddings against the wishes of the diocese, even if the school principal gives permission;
• the right for parents to remove their children from public school programs that don't accord with their values; and
• the creation of a "national religious freedom commissioner" within the Australian Human Rights Commission.

Although the Ruddock review was sparked by the legalisation of same-sex marriage, the churches said the issue of religious freedom was much broader, and it was a "completely false dichotomy" to claim religious rights were in conflict with LGBTI rights.

They conceded there was “nothing” in Liberal senator Dean Smith’s same-sex marriage bill which prevented people holding, expressing or teaching their religious beliefs. But there were still deep concerns about the “long term consequences of same-sex marriage” for religious rights, and the potential for future governments - state or federal - to undermine those freedoms.

"The new frontier is gender identity," the churches argued, deeming it a "new and popular" cause. It was also about "the normalisation of a particular, boundary-free attitude to consensual sexual conduct that conflicts with the moral values of a great many Australian parents".

The Ruddock inquiry was told extra protections for people of faith were necessary in an increasingly secular era in which there is "hatred against people of faith" and where "there is no longer a consensus that religious freedom matters".

The existing constitutional provision protecting the free practice of religion was too vague to be useful, the churches argued, and only restricted incursions on freedom by the federal government.

Professor Parkinson said a federal law to codify religious freedom "may be rarely invoked" against the states and territories, but would have a "more educative effect" as to the legal boundaries. It would be buttressed by section 109 of the constitution, which declares a Commonwealth law will prevail when in conflict with state law.

"I see it as quite a modest thing," Professor Parkinson said.

Mr Ruddock's inquiry will also receive submissions from the major Catholic dioceses and leading marriage equality campaigners.

It is due to report to Prime Minister Malcolm Turnbull in March.