Former National Cabinet minister Sir Douglas Graham was brought in to sort out the mess and in 2009 was critical of the earlier deal, calling the sale and leaseback terms neither commercially based nor transparent.
Other tribes have since joined the 13-member Tamaki Collective which is negotiating with the Crown over its shared interests including volcanic cones, as well as moving towards individual settlements.
The process has taken the sting out of what was a fraught Treaty settlement region.
Under the new terms, Ngati Whatua will pay the Defence Force $95.63 million over five years for five housing blocks.
Land at Narrow Neck will be sold for $13.8 million and another block at Wakakura Cres for $10 million.
The agreement sets out that housing land must be leased back for five years.
Most of the 250 homes on the land are occupied by families. Defence housing and property director Peter Bollmann said the Government's recent Defence white paper signalled it was "moving out of the business of providing rental housing for personnel".
"A new housing policy which was introduced in 2008 is based on the principle that service personnel and their families should live among the communities they serve."
Mr Bollmann said staff also wanted to have greater choices about where they lived.
"It is too soon to say what the housing options for personnel will be when the leaseback period ends in five years' time."
NGATI WHATUA O ORAKEI NAVY DEAL
Hapu to buy:
* Five New Zealand Defence Force housing blocks for $95.63 million. These will be leased back to the Crown for five years.
* Defence land at Wakakura Cres for $10 million.
* Defence land at Narrow Neck for $13.8 million.
* Deal vests a 33.64ha conservation area in tribe's name. To be used as a recreation reserve administered jointly by tribe and Auckland Council.
* Purewa Creek's name to be changed to Pourewa Creek.
* $18 million - $2 million already received through hapu's 1993 Railways settlement.
* Rights of first refusal for 170 years over surplus Crown-owned properties.