She said what was being done was "completely unique" to reinvigorate a city that had changed a lot over the years.
Ardern was welcomed with a powhiri and waiata to 'Site A' of the civic precinct. Tangata whenua and the Tauranga city council commissioners sat together to acknowledge the partnership being finalised today.
Ardern was accompanied by Labour MPs Stuart Nash, Tamati Coffey and Angie Warren-Clark.
Commission chairwoman Anne Tolley said she was "honoured" Ardern could attend the signing of the deed.
She acknowledged the late Peri Kohu in her speech.
"Peri was instrumental in the process that brings us here today."
Tolley said the connection of mana whenua to the site and the "long and complex" history of it was front of mind.
"We saw this as an opportunity to do the right thing and to act in a way that is respectful of the past and mindful of the future."
Tolley said the site would be redeveloped into facilities that local people would be proud of. It would also add "critical momentum" to 1.5b of private investment in the CBD and would help its economic revival.
The deed was signed by Tolley and Otamataha Trust chairman Puhirake Ihaka, ending the formalities.
Submissions received on new ownership structure
The new council-controlled organisation is called Te Manawataki o Te Papa Charitable Trust.
Seventy-three submissions on the proposal to establish a new ownership structure for the land were received during the consultation process that took place in September.
Of those, 50 were in support, 16 opposed, six did not support the proposal in its current form, and one did not provide feedback on the proposal, but supported the future development of Te Manawataki o Te Papa [the heartbeat of Te Papa].
The new organisation will be jointly governed by the council and Otamataha Trust. The Trust represents mana whenua from Ngāi Tamarāwaho, Ngāti Tapu and Te Materāwaho – direct descendants of those who originally released the land to the Church Missionary Society in 1838, to be held in a sacred Trust for the benefit of Māori and the church (community).
The new organisation will buy the land from the council for a nominal sale price of $1. The council will then lease the land back from the organisation on a perpetual "peppercorn lease" basis.
The site will be developed by the council over the next eight years to create the $304 million civic precinct Te Manawataki o Te Papa.
This will include a library, museum, exhibition centre and a civic whare [public meeting house], subject to achieving 50 per cent of the required funding from non-ratepayer sources.
The Te Manawataki o Te Papa Charitable Trust trustees are expected to be appointed before the end of the year.
In 1838, the land was acquired from mana whenua by the Church Missionary Society to be held for the benefit of Māori and the church, in the face of increasing land demand by settlers.
However, much of the area was reluctantly gifted by the Church Missionary Society to the Crown in the 1860s, despite the objections of mana whenua, who argued that if it wasn't to be used for its original purpose, the land should be given back.
'Site A' was eventually transferred by the Crown to the Borough of Tauranga in 1995, to be used for municipal buildings.
The alienation from the land that was experienced by mana whenua has been recognised by the Waitangi Tribunal as being undertaken in a manner that breached Te Tiriti o Waitangi and its principles.