The Aboriginal and Torres Strait Islander social justice commissioner says the alleged rape of a two-year-old in the Northern Territory is an "absolute tragedy" but warns there is no simple solution to the complex question of when children should be removed from their families.

The horror allegations have attracted national attention and reignited debate around when and how to remove kids from dangerous homes. They have also put the spotlight back on the disproportionately high number of Indigenous children in out-of-home care.

The issue is particularly fraught given the trauma experienced by the Stolen Generations and their descendants.

"We know that past policies of removal, of both Aboriginal and non-Aboriginal children from their families, have had devastating long-term effects," June Oscar, the Australian Human Rights Commission social justice commissioner, told Fairfax Media.