The Government says it will likely still maintain ownership of the land until it is sold on as completed houses, and it can put requirements around the pace and type of development.
Ngati Whatua's legal challenge had embarrassed the Government and threatened to hold up the construction of new homes.
Under Treaty settlement rights, the iwi had the right of first refusal to buy surplus Crown land, but there were exemptions including if the land is being used for "state housing purposes".
Ngati Whatua had sought a judicial review of whether the land's development fit that exemption. That legal question remains, but the agreement struck allows things to move forward.
Dr Smith said that the new agreement recognised that a right of first refusal over development of Crown land for state housing purposes was part of the Tamaki Collective Deed of Settlement, signed in 2012 between the Crown and Nga Mana Whenua o Tamaki Makaurau.
"The [new] agreement reinforces this protocol, [and] includes a shared commitment for 20 per cent of new houses delivered through the Auckland housing programme to be made available for purchase by community housing providers, and for a further 20 per cent priced as affordable for first home buyers."
Those social and affordable housing targets will be in place, whether iwi take up the chance to be developer or not.
Labour's housing spokesman Phil Twyford said Ngati Whatua had extracted "an excellent deal" for Aucklanders, that otherwise would not have occurred.
"This is a much better outcome than Nick Smith would have delivered...if he had any sense left at all he would have worked with Ngati Whatua from the start instead of stumbling and blundering his way into a court case."
Ngati Paoa, part of the Tamaki Collective, also welcomed the deal. Treaty negotiator Hauauru Rawiri said the iwi was committed to the development of social and affordable housing.
The Tamaki Collective is made up of Ngai Tai ki Tamaki, Ngati Maru, Ngati Paoa, Ngati Tamaoho, Ngati Tamatera, Ngati Te Ata, Ngaati Whanaunga, Ngati Whatua o Kaipara, Ngati Whatua Orakei, Te Akitai Waiohua, Te Kawerau a Maki, Te Patukirikiri and Te Runanga o Ngati Whatua.