A Mount Isa pastor is one of three authors of a document calling on prime minister Scott Morrison to scrap vaccine passports.
A letter called the Ezekiel Declaration is demanding Scott Morrison to allow them to have vaccinated and unvaccinated people in their congregations.
The letter said church leaders had "significant concern" at the prospect of vaccine passports, which the authors claim would "inflict terrible consequences" on Australia.
The letter is signed by 3000 church leaders and written by three: Mount Isa Baptist Church senior pastor Timothy Grant, New Beith Baptist Church senior pastor Matthew Littlefield and Biota Baptist Church senior pastor Warren McKenzie.
Pastor Grant and the others say vaccines risk creating a two-tiered society.
They also argue that people are already under stress, conscience should not be coerced, vaccines don't make "logical sense" in protecting others, and Christian leaders find it untenable to refuse entry to people who want to attend church.
"For many Christian leaders and Christians, this is an untenable proposal that would inflict terrible consequences on our nation," the letter read.
"We as Christian leaders find it untenable that we would be expected to refuse entry into our churches to a subgroup of society based on their medical choice. Only our precious Saviour, Jesus Christ, has the authority to regulate the terms of corporate worship. These terms tell us that we are to make no distinction between those who call out in faith, neither on race nor medical choice."
The government has not yet made a decision on whether vaccine passport would be mandatory for church attendance but the Prime Minister has described extra freedoms for fully vaccinated Australians as "common sense".
The the first international travel vaccine passports arrive next month.
The first international immunisation passports are set to be rolled out in October with all vaccines approved by Australia's medicines regulator recognised for inbound travel and immunisation information could automatically be linked to Australian passports for people entering the country.
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