Australia's peak advocate for Aboriginal children has described the circumstances around child protection in the Northern Territory as "dire", following the shock resignation of the Territory's children's commissioner.

Shahleena Musk, who was appointed as children's commissioner by the former Labor government in late 2023, announced she would be stepping down from the role in a statement released late on Thursday afternoon.

Her decision came the day after a government-dominated parliamentary scrutiny committee greenlit amendments to the Territory's child protection laws, despite widespread criticism of the bill.

In her statement, Ms Musk said her decision had "not been made lightly" and reflected her "growing concerns" around transparency and consultation in the NT government's decision-making.

She said she was unable to support what she described as "substantial and wide-reaching changes to child protection laws" and that she was concerned by her "effective sidelining" during the process.

Resignation 'a tragedy' for NT children

The National Commissioner for Aboriginal and Torres Strait Islander Children and Young People, Sue-Anne Hunter, said she was "saddened" by the news, and described the "circumstances" in the NT as "dire".

"The fact that we have a commissioner for Aboriginal children stepping down from a role due to actions of the current NT government shows firsthand the lack of care and accountability they have towards our people," Ms Hunter said.

Ms Hunter called on the government to "listen to the experts" and "pause" the proposed child protection bill in its current form.

Over the course of her two-and-a-half years as children's commissioner, Ms Musk has been vocal about policy changes affecting young people, including the lowering of the age of criminal responsibility and changes to the Territory's youth justice laws.

A year ago, Ms Musk spoke about changes that removed detention as a last resort for young people and tightened bail laws, and expressed frustrations about a lack of consultation with her office and other key stakeholders.

"There's an unwillingness to work with me and others," she said at the time.

"There's clearly a belief that they've got a mandate to be tougher on these young people, but the evidence goes against that."

In May, the Office of the Children's Commissioner NT released a report into allegations of harm and exploitation suffered by children in care, which found there had been more than 400 notifications of alleged harm against children in the system over a year between 2024 and 2025.

Last month, Ms Musk became emotional while giving evidence at a public hearing hosted by the NT Legislative Scrutiny Committee into the child protection changes.

Independent member Justine Davis said Ms Musk's resignation was "incredibly disappointing" for the Territory and "speaks volumes" about the current political environment.

"[The commissioner] took an oath and she's not able to fulfil that oath, and that's a tragedy for Territory children," Ms Davis said.

"There's an ongoing pattern of this government of sidelining critique, of not listening to people who have different views to them."

The head of one of the Territory's biggest legal organisations, the Northern Australia Aboriginal Justice Agency (NAAJA), echoed the concerns.

"I think it should be of concern for all of us when some of our best talent and most experienced people decide that it's no longer tenable for them to fulfil the duties that they're required to perform," NAAJA chief executive Ben Grimes said.

"The government seems to be displaying a pattern where scrutiny, accountability, robust debate is seen as a hindrance to good decision-making rather than an asset to good decision-making."

Minister rejects claims around transparency

In a scathing response, NT Minister for Children and Families Robyn Cahill rejected Ms Musk's claims, insisting there was adequate transparency around the government's changes.

"The commissioner lodged a submission to the Legislative Scrutiny Committee, appeared before it and had her views heard in public, as every other stakeholder did," Ms Cahill said.

The scrutiny committee received 150 submissions on the proposed child protection bill.

In her foreword to the 169-page report, CLP committee chair Oly Carlson acknowledged "many" submissions and witnesses opposed the changes, but the committee ultimately recommended the bill be passed as drafted.

"If Ms Musk were genuinely concerned about this, then the last thing she would be doing is walking away," Ms Cahill said in her statement on Friday.

Ms Davis described Ms Cahill's comments as "deeply offensive" and a "continuation of a pattern of inappropriate personal attacks on the children's commissioner by this government".

"The CLP's treatment of Ms Musk, and the minister's response to her resignation are representative of a government who view themselves as above accountability," she said.

Secretariat of National Aboriginal and Islander Child Care (SNAICC), Catherine Liddle, said the response was a "political distraction" from the central issue of child protection.

"You cannot claim to care about the wellbeing of children and ignore the evidence about what actually keeps children safe," she said.

Ms Liddle described Ms Musk as a "fearless and courageous" commissioner and called on the NT government to replace her with an Aboriginal or Torres Strait Islander person.

She also encouraged the government to bolster the powers of the children's commissioner to improve the policy-making process.

"Strengthen the powers of the commissioner so they genuinely have the ability to not only shine a light into where things in the system are failing children … but also to work alongside the government to improve the system," she said.