The demonstrations, which took place in Melbourne, Brisbane, Adelaide, Canberra and Sydney, focused on the harm British colonisation caused Indigenous Australians.
Australia is one of the few former British colonies that never struck a treaty with the Indigenous population.
Footage was shared on social media of the Union Flag being burned at a park in Melbourne – the starting point for a lunchtime Abolish the Monarchy march.
In Brisbane, Wayne Wharton, an Indigenous protester, said of the Queen: "She signed during her time of reign was, if you go back to the legal documents and all the documents that incarcerated our people, it was her signature that was on them, and so she's not innocent in no way shape and form."
Indigenous people's responses in Australia to the queen's death have been mixed. On the same day as the protests, Indigenous dancers and singers from the started a memorial service at Canberra's Parliament House.
Two opinion polls published since the queen's death show most Australians want to remain a constitutional monarchy.
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Advocates for an Australian republic argue that this is a temporary reaction to the intense media coverage of a popular monarch.
Governor-General David Hurley, King Charles III’s representative in Australia, acknowledged that the monarch's passing had prompted different reactions amongst Australians.
“I’m conscious to respect that the response of many First Nations Australians is shaped by our colonial history and broader reconciliation journey, that is a journey we as a nation must complete,” he said.
Australian lawmakers paid tribute to Queen Elizabeth on Friday, when parliament reopened after a break taken to observe the monarch's death.
Prime Minister Anthony Albanese said the Queen was "a rare and reassuring constant amidst rapid change”.
Albanese has previously said he wants an Australian president to replace the British monarch as the nation’s head of state, although he has avoided getting entangled in the republic debate since the queen's death.
Other lawmakers, however, weighed in on the discussion.
Adam Bandt, leader of the small Australian Greens party, expressed his condolences but added: “The queen’s passing means that we get a new head of state without having any say in the matter. It is absolutely the appropriate time to talk respectfully about whether that is right for us as a country.”
The Queen officially opened Parliament House in 1988. Her father opened a temporary Parliament House nearby in 1927. King George VI was then Duke of York, making his daughter the first reigning monarch to visit Australia.
Queen Elizabeth II visited Australia 16 times during her time as queen.