The dual leader model at the Human Rights Commission honours Te Tiriti o Waitangi and is what the public wants, the commission's chief executive says.
The commission has just introduced a co-chief executive position, appointing Julia Amua Whaipooti to the role on Wednesday.
Whaipooti is an expert on the Treaty and the rights of Māori and will start in the new year.
The commission says no new funding was needed to establish the role.
Justice Minister Paul Goldsmith thinks having dual leaders in the public sector is not appropriate.
Human Rights Commission chief executive Meg de Ronde told Morning Report the commission is a Treaty based organisation and requires partnership between Māori and Pākehā.
"This is part of a commitment to a Te Tiriti based organisation which is really crucial if you're working in human rights in Aotearoa because Te Tiriti o Waitangi is our founding human rights document so it's what gives us rights and duties to each other and it's really important in terms of our legislation as well."
The decision was not taken lightly, she said.
"But what's been missing from some of the political rhetoric flying around is we've actually disestablished a deputy role so I won't have a deputy, I'll have a shared leader to work alongside and we're really excited to bring this new model to fruition," she said.
"What we're hearing from New Zealanders, and we've recently done some polling on this, what's not sustainable is divisive rhetoric around race and New Zealanders are really calling for a reasoned and respectable approach, they're calling for Māori and Pākehā to work together.
"So what we're trying to do with this model is to walk that talk."
The ACT Party said Whaipooti's appointment was "just the latest example of a taxpayer-funded bureaucracy serving itself at the expense of delivery for New Zealanders".
The new government wants to change the inner-workings of the Human Rights Commission.
Justice Minister Paul Goldsmith has said he disagrees with the organisation's staffing allocations and is also refusing to express confidence in the agency's Chief Human Rights Commissioner Paul Hunt.
He has confirmed he plans not to reappoint Hunt, whose warrant expires in January.
"The government will not be reappointing Chief Human Rights Commissioner Paul Hunt and are starting the process to find his replacement," he said in a statement.
ACT is reigniting calls for the commission to be abolished entirely.
Goldsmith said he was not planning to do that but said the government was planning on making changes across the commission.
The Human Rights Commission is Crown funded but independent and governed by the Paris Principles, de Ronde said.
Monday will be the 75th anniversary of the Universal Declaration of Human Rights.