Whanau Ora will be governed by a new Crown-iwi partnership group and three non-government organisations will be set up as part of the process, the Government has announced.
The new partnership group will be made up of senior ministers, iwi leaders and experts.
Minister for Whanau Ora Tariana Turia said three non-government commissioning agencies will be established, one in the North Island, one in the South Island and one Pacific agency and will be ready by next July.
"This new commissioning model signals the wind down of the regional leadership groups at the end of December,'' Mrs Turia said.
"The governance group will also be wound down.''
Mrs Turia said Te Puni Kokiri will lead the charge with the changes.
Te Puni Kokiri chief executive Michelle Hippolite said she was confident about the transition to the new model.
It is believed the new structure could escape the scrutiny of the Official Information Act.
Asked how it would be held accountable if it did, Mrs Turia said families would provide scrutiny.
Mrs Turia told a packed audience at Wharewaka on Wellington's waterfront that decisions and changes in Whanau Ora should come from the community.
"One of things that I feel very, very strongly about is that we must not let an agencies define Whanau Ora - that is in your hands,'' she said.
NZ First leader Winston Peters criticised the programme, saying Te Puni Kokiri was being sidelined in favour of the three NGOs.
"The millions of dollars being spent by Whanau Ora thus far simply will not stand up to public scrutiny. Dishing out money for family reunions, rugby club functions and for gangs to buy drugs is an appalling misuse of taxpayer money and is only happening so the Prime Minister can try and prop up one surviving support party for the next election.''