Prime Minister Malcolm Turnbull announced the commission following shocking footage of boys being stripped and tear-gassed at the Don Dale Youth Detention Centre in 2014.
Co-commissioners Mick Gooda and Margaret White are investigating incidents over the past 10 years since the Territory introduced the Youth Justice Act.
But on the first day of hearings, the commission's very existence was questioned, with authorities urged to take urgent action to reform the system.
Images revealed earlier this year of teenager Dylan Voller hooded and strapped to a chair at the Don Dale detention centre in Darwin caused international outrage.
The fallout has been widespread, with the Territory's Country Liberal Party Government sacking Corrections Minister John Elferink before, itself, losing the elections to Labor.
On day one of the public hearings at Darwin's Supreme Court, the court heard government child abuse reports on youth detention in the Territory were dismissed without investigation.
The Senior Counsel Assisting, Peter Callaghan, has questioned whether inquiries and investigations are becoming a substitute for action.
He referred to a number of inquiries over the past 10 years, including more than 50 reports with recommendations relevant to the inquiry.
"Do we need to confront some sort of inquiry mentality in which investigation is allowed as a substitution for action and reporting is accepted as a replacement for results? The bare fact that there has been so much said and so much written over such a long time is suggestive of a persistent failure that should not be allowed to endure."
National Children's Commissioner Megan Mitchell says she had visited Darwin's Don Dale youth detention centre earlier this year.
She told the inquiry what she saw was extremely concerning.
"When I asked the young people how they felt in that environment, some of the words they said were 'depressed,' 'angry,' 'sad,' 'like a caged animal,' and, if you go to that maximum security area, you will understand why they feel like that."
Concerned members of the community, like this one, say they are worried the royal commission will achieve nothing.
"This is the third royal commission I have been involved in, from black deaths in custody, to the removal of children, and now this, the treatment of our youth, our developing nation. You know, when does it stop? This is the third now. Are we to consider this is going to be third time lucky or three times and you're out, three strikes and you're out? I've got my bet on which one it's going to be."
Federal Indigenous minister Nigel Scullion put forward a proposal this week to send juvenile offenders to the Mataranka pastoral station as an alternative.
Speaking in the wake of what he calls the "Don Dale disaster," he pointed to the Indigenous Land Council as a possible source of help.
"My offer was simply to use Mataranka. We have the ILC. We have extremely good training systems within that. And I've offered to be able to build a level of amenity to the international best standard and to actually lead the way that Australia needs to take."
Meanwhile Dylan Voller, the youth at the centre of the shocking footage, remains in an adult jail just outside Darwin.
His mother, Joanne Voller, says he has been in constant detention from the age of 12, with only nine months out, because of behavioural issues which were not addressed.
She is calling for him to be released and re-engaged within the community.
The 19-year-old is expected to give evidence to the commission in November.
But speaking at a public demonstration against the treatment of Indigenous youth in detention, Joanne Voller said she fears for her son's safety.
She says she is worried he will not be able to speak freely to the royal commission.
"I'm concerned that he'll become the next Aboriginal death in custody, I guess. That's my biggest concern, because, if so much can happen already, and he's still sitting in the place, and he's got to go and give evidence, you know ... like, yeah, I'm fearful. I'm scared that his name, on the list of the people that have already passed away, been shot by police, have died in custody, I'm scared that my son will not just be the person that survived. I'm scared that, while he's still in custody, he's going to be the next person whose life's gone."
The royal commission's final report is due to be delivered by the end of March next year.
