The sites were protected under the Tauranga City Plan and there were no plans to remove those protections, he said.
Larking said the archaeologist was accompanied by cultural monitors from Tapuika, Ngā Potiki and Ngāti Pūkenga when the bones were found exposed at three separate sites.
They were identified as human by the archaeologist.
"In accordance with tradition, the bones were not moved from where they were found," Larking said.
"Loose sand was placed over the exposed bones and the cultural monitors performed a karakia after each discovery."
It was not the first time bones had been found in the dune system over years of investigations going back to 2000, and the recent find was "not unexpected", he said.
However, the assurances of council protection were not enough for Renee Ritete, one of the landowners in the Te Tuma Kaituna 14 block.
She believed the council was "hellbent on putting a town on this land" and did not trust them to properly protect the cultural significance of the area, believing the project should be led by iwi instead.
"The council needs to step back and stop trying to control everything."
The way the koiwi were found - exposed out of the ground - told her "the dead have something to say" and she did not think the council had the expertise to hear their message.
Heritage New Zealand archaeologist Rachel Darmody said the find had been reported and the site was protected under the Heritage New Zealand Pouhere Taonga Act 2014.
Heritage New Zealand would be involved in any proposal to modify the sites.
Te Tumu development
- Housing for 15,500 people
- $60m in infrastructure costs
- House builds expected to start in 2021
- Located between Waiarakei and the Kaituna River
- Structural planning and community consultation under way.
Source: tauranga.govt.nz/our-future/projects/te-tumu