Demonstrators gathered in Melbourne, Sydney and Brisbane to express shock at footage showing indigenous boys being tear-gassed.
The video also shows a boy wearing a "split hood" while cuffed to a chair.
Australia's Prime Minister, Malcolm Turnbull, has called for an investigation.
However, he rejected calls for a broader national inquiry.
Around 700 people rallied in Melbourne and 300 in Sydney, according to Reuters.
Footage of the abuse first emerged on national broadcaster ABC's Four Corners programme.
Filmed at the Don Dale youth detention centre in the Northern Territory, the programme focuses on the treatment of Dylan Voller, who was assaulted, stripped naked and kept in solitary confinement aged 13 and 14.
At one stage he was strapped to a restraint chair while wearing a hood for almost two hours. He was also among a group of six children who were subdued with tear gas.
The United Nations Human Rights Commission said it was shocked by the footage.
"We encourage the Government to extend the scope of the investigation... to establish that such appalling treatment is not taking place in any other place of detention in Australia," it said in a statement - adding that authorities should compensate the children.
The six boys are seeking damages for mistreatment, according to ABC.
Indigenous people represent about 3% of Australia's population but are 26 times more likely to be in detention than non-Indigenous youth, according to theAustralian Institute of Health and Welfare.