"As part of the protocol, the project archaeologist is leading the process in close collaboration with Ngā Hapū o Ōtaki.
"The area was blessed by representatives of Ngā Hapū and work in that area has stopped to allow for the careful removal of koiwi and further investigations."
Thackwray said the koiwi was "being cared for and treated with the respect they deserve in a secure environment under the supervision and auspices of Ngā Hapū".
"Once site investigations are complete, the koiwi will be reinterred by Ngā Hapū o Ōtaki.
"Investigations are currently ongoing but we expect to be able to confirm details about the discovery in the coming weeks, including the exact number of koiwi discovered."
The discovery had not resulted in delays to the project.
The agency is creating a four lane expressway between Peka Peka and Ōtaki at an estimated cost of $330 million.
The expressway, projected to be finished in 2021, will remove congestion points, create reliable journey times, improve safety, and improve economic productivity.