Protesters have been urged to call Prime Minister Malcolm Turnbull's office and leave a "clear message" that asylum seekers are welcome to remain in Australia.
"Let them stay, let them stay," a colourful bunch of thousands chanted in central Sydney on Monday evening, while in Melbourne a similarly large crowd packed the front of the state library waving signs like "Open the Borders".
The Stand for Sanctuary rallies organised by GetUp! were also held in Brisbane, Adelaide, Perth, Darwin, Hobart, Canberra and regional centres across the country.
The protests come after the High Court last Wednesday validated Australia's offshore processing regime, which means 267 asylum seekers - including 91 children - who are in the country for medical treatment could be sent to Nauru.
While the government has not made a decision to deport them, advocates have pleaded for sympathy and thousands have turned out at Monday night's protests to voice their concerns.
At least 10 Anglican churches across the country, led by the Anglican Dean of Brisbane, Peter Catt, have offered sanctuary to the 267 people.
Actor Imogen Bailey implored the Sydney crowd to phone Mr Turnbull's office and leave a message.
"Our message is 'we want to let them stay'," she said.
Those rallying in Melbourne joined in a mass chant as GetUp! organiser Sally Rugg left a similar voicemail for the prime minister.
About 400 were expected at the Brisbane protest, which unlike the noisy Sydney and Melbourne events, will take the form of a silent reflection at St John's Cathedral in the city.
A record crowd marched through Darwin, with more than 300 people gathering along the Nightcliff foreshore.
"We can show mercy to these people, we can show compassion to them, we can do something vastly different from the terrible treatment they have experienced," paediatrician Dr Josh Francis told the crowd.
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