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.