An overwhelming majority of the Synod backed a motion calling on state and territory leaders to protect religious freedom in light of concerns that such rights are being eroded in society.
South Sydney bishop, Robert Forsyth, who brought forth the motion said such freedom was at risk of being undermined "due to a focus on other, sometimes competing, rights."
"I would like us to move from this culture where we are supplicants seeking exemptions to where our governments, state and federal, saw religious freedom as a positive good," he said.
Bishop Forsyth also argued that religious exemptions were separate from anti-discrimination laws, explaining that they were sought not to exclude people, but to allow religious groups to "exist and operate in accordance with their unique cultures and beliefs."
Religious freedom in Australia has been tested in recent years, as seen in the ongoing case Christian Youth Camps V Cobaw.
Earlier this year, CYC's appeal against the ruling that they had discriminated against the group supporting same-sex attracted youth by not providing them with accommodation was dismissed by the Victorian Court of Appeal.
The CEO of Anglicare WA, Ian Carter, labelled the 'gagging' of faith-based organisations as a fundamental issue.
"Anglicare delivers services to one in 40 Australians. We have a proud history of work in virtually every community around this country," he said. "We should not be held back just because we deliver service, to also not be able to advocate for the people for which we work."
The Primate will now bring the resolution to the Prime Minister and State and Territory leaders.