"We will treat the site with the utmost care and respect to ensure the correct cultural practice is carried out," says Hunt.
Crown Maori/Relations Minister Kelvin Davis said it was a significant discovery that would grow understanding of where and how waka were made.
"It reinforces traditional korero around the use of resources including waka forests, where particular trees were identified and nurtured for waka construction."
Excavation of the waka is underway with consultation of project treaty partners Hokai Nuku, Heritage New Zealand Pouhere Taonga and Auckland Council.
Hunt said the object would be lifted into a storage container and taken to a new site under the close supervision of Hokai Nuku and Heritage New Zealand to be examined more closely and preserved.
It is not yet known how old the waka is, who it belonged to or how it came to be left in an unfinished state.