Federal legislation has passed through Parliament increasing the independence and powers of the National Commissioner for Aboriginal and Torres Strait Islander Children and Young People.

The legislation introduced by the government last month passed the Senate on Wednesday, having previously passed the House of Representatives, and was welcomed by advocates including SNAICC - National Voice for Our Children.

Last year, Wurundjeri and Ngurai Illum Wurrung woman Sue-Anne Hunter became the first full-time National Commissioner for Aboriginal and Torres Strait Islander Young People, and the new legislation formalises the role, entrenching the National Commission as an independent statutory agency.

The proposal divided opinion in Parliament, with Senator Jacinta Nampijinpa Price arguing the legislation would add bureaucracy without delivering real change.

SNAICC described the passage of the legislation as "a critical step toward stronger accountability for outcomes affecting Aboriginal and Torres Strait Islander children".

Minister for Indigenous Australians Malarndirri McCarthy said the changes were "important because we are listening to what the communities have been asking (for) for a long time".

Senator McCarthy said 70 organisations gave guidance on the legislation and the need for a National Commissioner was a consistent theme.

"There needs to be a role where the national First Nations Commissioner is there for the children who are being taken away, who are in out of home care," she said.

"We've seen those figures rise staggeringly, especially in states like Victoria, and having the ability for the National Children's Commissioner to be able to work with each state and territory (and) inform this parliament is absolutely critical."

The Greens proposed two amendments - moved by party leader Larissa Waters - including provisions to raise the age of criminal responsibility to 14 years, and another requiring the Minister to provide a response to recommendations made by the Commissioner - also to give reasons when a recommendation is not accepted.

Senator Waters told the Senate as a "matter of courtesy, if nothing else, the government should be obliged to respond to the recommendations that the commissioner makes to Government".

The amendments were not passed.

SNAICC chief executive Catherine Liddle said the legislation delivers on decades of advocacy from Aboriginal and Torres Strait Islander communities and the community-controlled sector for a truly independent, legislated Commissioner.

"This is a moment we have fought for over many years," Ms Liddle said.

"For decades, SNAICC and our partners have advocated for a National Commissioner with real powers. Someone who can stand independent of government and hold systems to account for the outcomes experienced by our children.

"By legislating this role, the National Commissioner now has the authority to safeguard commitments to our children and families, so they are delivered."

Ms Liddle said the legislation enables the Commissioner to act independently, initiate inquiries into systemic issues and elevate the voices of Aboriginal and Torres Strait

During Upper House debate, One Nation Senator Malcolm Roberts claimed the Commissioner will have a negative effect on efforts to improve the lives of First Nations people and communities.

"It won't help. It'll hamper and hurt, because the aim is to look good, not do good," he said.

In response, Senator McCarthy urged Senator Roberts and his party "to get on board... because what Commissioner Hunter will be able to do... (knowing) that she has the support of this Parliament behind her to work with our kids across the country".

After the passage of the reforms, Ms Liddle noted that "with Aboriginal and Torres Strait Islander children still ten times more likely to be in out-of-home care, and the links between child protection and youth justice continuing to grow, the need for strong, independent oversight has never been more urgent".

"This legislation backs in Commissioner Sue-Anne Hunter, strengthening her ability to be a fearless advocate and drive real change for our children.

"We look forward to working with Commissioner Hunter, who is already having a strong impact in elevating the voices of Aboriginal and Torres Strait Islander children and driving attention to the issues that matter most."

SNAICC said the legislation reflects a long-standing priority of the Family Matters campaign and aligns with key national reform efforts, including Safe and Supported: Australia's ten-year national framework for child and family wellbeing.

With additional reporting by Dechlan Brennan.