Protesters say they will continue holding demonstrations "until there is justice".
Australians have marched in the streets of Brisbane, Darwin, Perth, Adelaide, Cairns and Kempsey amid continuing global anger over the death of African-American George Floyd at the hands of police.
Coronavirus restrictions have been eased, allowing for the protests to be authorised.
Fewer than a thousand people have gathered for a Black Lives Matter protest in Brisbane city, leaving organisers disheartened by the poor turnout.
The rally against First Nations deaths in custody comes just a month after about 30,000 Queenslanders rallied following the death of African American man George Floyd.
"I can not explain the disappointment," Gomeroi Kooma woman Ruby Wharton told the small crowd gathered at King George Square on Saturday.
"It was okay for people to come out here and want to be a part of it when they were chasing a hundred likes on Instagram."
"That is shameful and tokenism," she said.
Organiser Bogaine Spearim told reporters the rally was intended to be a continuation of the global protests that kicked off in the wake of Mr Floyd's death in May.
"Deaths are continuing to happen in Australia - Dave Dungay Jnr said 'I can't breathe' before dying in custody," he said.
"We will continue to hit the streets and disrupt until there is justice."
Mr Dungay died in 2015 after he was restrained by five prison officers in Sydney's Long Bay jail after he refused to stop eating biscuits.
Garrwa and Butchulla man Fred Leone called on the Queensland government to conduct a broad review into black deaths in custody.
"Black Lives Matter. They do not just matter cause it is trending, they matter every single day."
More than 430 Aboriginal and Torres Strait Islander people are known to have died in custody in Australia since a royal commission into Aboriginal deaths in custody delivered its final report in 1991.
Organisers are also calling for anti-racism training in schools and an end to racial profiling by police.
In Adelaide, organisers said the rally comes at a historic moment in the fight against systemic racism.
"In Australia, we see mining corporations destroying historic sites while Aboriginal communities are forced through the humiliation of cashless welfare," they said on Facebook.
"Other black and migrant communities also face over-policing, job discrimination and social inequality."
In Perth, hundreds gathered for the city's third major Black Lives Matter protest, calling on the Western Australian government to put the same level of energy into ending systemic racism and institutionalised violence as it has in protecting the community from COVID-19.
Several young speakers passionately addressed the physically distanced and mask-wearing crowd, which repeatedly chanted "black lives matter", with numbers well down from the thousands rallying in the city previously.
As they marched through the city, protesters held the Aboriginal flag and signs, including some that read "Systemic racism exists here too" and "White silence equals violence".
Among the speakers was Keith Tapiwanashe Makuni, who told the protesters it was time for positive change.
"We are the future leaders," he shouted.
Mr Tapiwanashe Makuni commended Premier Mark McGowan for the WA government's efforts to keep the state safe during the pandemic, including keeping the borders shut.
He said the premier should put the same amount of energy into fighting systemic racism and ensuring equality for everyone.
"To those who don't want change ... please, close your borders to them," he said.
"We want a new era. We want empowerment. We want equality. We want fair treatment.
"Change is in young people ... change is within us. Together, we can do it."
Earlier on Saturday, Mr McGowan told reporters the lifting of coronavirus restrictions meant rallies were allowed, compared to one month ago when he advised caution.
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