Police confirmed there have been two separate discoveries of human remains since earthworks began in early May.
In 2019, the Greater Wellington Regional Council identified a serious risk to the coastal edge of Queen Elizabeth Park.
The old building had been demolished because of coastal erosion caused by climate change.
The development plan started six weeks ago but had stopped because of the discoveries.
Ecosystems and community manager David Boone said the kōiwi are of significance to Ngāti Toa.
"It's a long-standing area that has been used by Ngāti Toa and Ngāti Haumia ancestors," he said.
"It was really no surprise that there was evidence of activity in the site from the pre-settlement era."
Ngāti Toa declined to comment to RNZ.
Police said both discoveries have been referred to the coroner.
The rebuild has since resumed.
RNZ
