The asylum-seekers, who were brought to Australia from Nauru mostly for medical reasons, number more than 260 and include 37 babies born in the country and 54 other children, advocates said.
The Anglican Dean of Brisbane, the Very Reverend Peter Catt, said the churches were reinventing the "ancient concept of sanctuary" by opening facilities such as St John's Cathedral in Brisbane to the asylum-seekers.
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Catt told the Australian Broadcasting Corporation the concept of sanctuary was not tested under law, "but my hunch is that if the authorities chose to enter the church and take people away, it would probably be a legal action".
He added: "So this is really a moral stand and it wouldn't be a good look, I don't think, for someone to enter a church and to drag people away."
Asylum-seekers, including children, who try to reach Australia by boat are sent to off-shore detention centres in Papua New Guinea and Nauru, where they can be held indefinitely while refugee applications are processed.
They are blocked from being resettled in Australia even if found to be genuine refugees.
Many of the asylum-seekers who were brought to Australia from Nauru are being held at Wickham Point, a secure facility near Darwin in northern Australia, raising questions about how they would reach Brisbane or elsewhere.
The High Court ruled Wednesday that the detention of asylum-seekers on Nauru did not breach domestic law, meaning the potential refugees could be returned there in the coming days.
Across Australia, thousands of people protested Thursday against the possible off-shore transfer of the asylum-seekers, carrying signs reading "(Prime Minister) Malcolm Turnbull #LetThemStay".
Australian Churches Refugee Taskforce's Misha Coleman admitted it would be difficult to move the detained asylum-seekers to the sanctuaries but said if they were, the cases would be managed "in a very sort of confidential way".
Police raid Save the Children offices in Nauru
Immigration Minister Peter Dutton said the churches had the right to their opinion but were not above Australian law.
The churches' stance came as the nation's human rights chief said children being held at Wickham Point suffered high levels of mental illness.
Human Rights Commission head Gillian Triggs said a medical team led by the government-funded body found that "34 per cent of the hundreds of children we visited had severe to moderate mental illness compared with two percent for children in the Australian community".
Of the children aged over eight years previously held in Nauru, 95 percent were assessed as at risk of post-traumatic stress disorder, the report released Thursday said.
"These children, most of whom had spent months in Nauru, are among the most traumatised we have ever seen in our 50 years of combined professional experience," Elizabeth Elliott, one of the paediatricians who accessed the children in October last year, added in a statement.
The United Nations human rights agency warned Wednesday that Australia was at risk of violating its obligations under international law if the asylum-seekers were transferred to Nauru.
Canberra has defended its policy as necessary to prevent the deaths of asylum-seekers at sea.
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