Up to 10 Anglican churches around Australia are offering sanctuary to about 270 asylum-seeks at risk of being returned to Nauru in the wake of a failed High Court challenge.
The offer is being led by the Anglican Dean of Brisbane, Peter Catt.
Dr Catt has declared Brisbane's St John's Anglican Cathedral a sanctuary for those who've suffered trauma and risk abuse if returned to the offshore detention centre on the Pacific Island nation.
"Nevertheless we are determined to apply its moral precepts and protect the most vulnerable from certain harm."
The offer coincided with a warning to the federal government from the United Nations refugee agency that it must consider the best interests of children in immigration detention.
Immigration Minister Peter Dutton says the cases of 267 people impacted by a High Court's validation of Australia's offshore processing regime will be individually considered on medical advice.
Dr Catt said there was irrefutable evidence from health and legal experts that the circumstances asylum seekers, especially children, would face if sent back to Nauru were tantamount to state-sanctioned abuse.
"This fundamentally goes against our faith, so our church community is compelled to act, despite the possibility of individual penalty against us," he said.
Sanctuary is a religious concept similar to asylum and dates back to the Old Testament.
Churches have traditionally been considered places of refuge for people seeking protection.
The legality of sanctuary has never been tested under Australian law.
"Nevertheless we are determined to apply its moral precepts and protect the most vulnerable from certain harm," Dr Catt said.
UN High Commissioner for Refugees spokesman Rupert Colville said asylum seekers were in a fragile state and may have mental health issues.
"Of course being sent back to this situation may just make them worse," he told ABC Radio.
Returning them to Nauru could be a breach of the convention against torture which covered cruel, inhumane or degrading treatment.
Mr Dutton reiterated his intention not to put any children in harm's way.
"We have to be compassionate on one hand but we have to be realistic about the threat from people smugglers," he told ABC Radio.
"We're acting in the best interests not only for these children but children that would follow them."
The Australian Human Rights Commission said the court's decision did not alter Australia's international obligations.
"Australia has obligations under international human rights law to protect the safety and wellbeing of all people under our jurisdiction, including people seeking asylum," commission president Gillian Triggs said.
The responsibilities remained whether or not third country processing was authorised by Australian law.
The Refugee Council said the ruling did not compel the government to return innocent and vulnerable people to Nauru.
The Asylum Seeker Resource Centre is co-ordinating silent protests around the country today.
The hashtag #LetThemStay is the catch-cry for the protests, held today in Sydney, Melbourne, Canberra and Adelaide, and tomorrow in Brisbane.
Anglican churches offering sanctuary
St John's Anglican Cathedral, Brisbane
St Cuthbert's Anglican Church, Darlington, WA
Perth Wesley Uniting Church
Gosford Anglican Church, Sydney
Pilgrim Uniting Church, Adelaide - St John's Uniting Church Essendon`
Paddington Anglican Church, Sydney
Pitt Street Uniting Church, Sydney
Wayside Chapel, Sydney