Ardern said it was a "big job" to eliminate unconscious bias against Māori in New Zealand.
She said the new legislation for Oranga Tamariki, set to come into force on July 1, meant that every effort should be made for uplifted children to be kept in the wider family.
The ministry has been under fire since it tried to take a 6-day-old baby boy from his 19-year-old mother at Hawke's Bay Hospital on May 6 because it said the child's wider family had a background of domestic violence and drug use - a claim disputed by the whānau.
Supporters tried to stop the baby being taken, police were called to the hospital and the ministry backed off, but the case is still going through a Family Court process.
The May 6 attempt was filmed by Newsroom.
Children's Minister Tracey Martin traveled to Hastings over the weekend to meet with local iwi Ngāti Kahungunu and the Māori Council about recent actions by Oranga Tamariki.
An internal inquiry is now being conducted, but Martin told Morning Report that it might include sensitive details about the family, and it would be up to them to release those aspects of the report to the public.
Martin said that nobody wanted the ministry to uplift three babies a week, and the interests of the child were always at the centre of any such action.
New legislation aimed at implementing a new approach for Oranga Tamariki was coming into force from July 1, and Martin said the $1.1 billion in the Wellbeing Budget for children was aimed at bringing out that change, including greater emphasis on working with iwi.
She said there was as much "institutional racism" in Oranga Tamariki as there was across New Zealand, and the ministry was working hard to address that.
Asked whether the uplifts represented a "stolen generation", Martin said the phrase "totally misrepresents" what was now happening between Oranga Tamariki and iwi.
She added: "Using that phrase is inappropriate in my view ... It completely devalues what happened to the Aboriginal people of Australia, which was set in legislation to destroy their culture."
Children's Commissioner Andrew Becroft told Morning Report that the use of that phrase was understandable.
"Maori children in care have increased and are increasing since 2000 consistently. Babies removed at birth have gone from two a week to three a week in the last four years, although dropped ever so slightly last year.
"You can well understand why people use that term. Alarm bells should be going off throughout New Zealand when that term, coined in Australia with a different legislative setting, is being applied here.
"We cannot shrink from the fact in New Zealand that there's a long term legacy of colonisation that exists and disadvantages Maori, and there's modern day unconscious bias and systemic disadvantage."
He said the Oranga Tamariki legislation was "nothing short of a revolution", setting up a preventative approach rather than a reactionary one.
"The change isn't yet being seen across the country. That's the challenge."
The Office of the Children's Commissioner is doing a wider independent investigation into Oranga Tamariki's uplifts of Māori babies aged up to three months old.
