Human bones have been discovered as part of the Peka Peka to Ōtaki Expressway excavation works.
NZ Transport Agency senior manager Andrew Thackwray said the discovery was made on June 12.
"Work was immediately ceased, the site closed and the accidental discovery protocol was actioned, as outlined within the contract consent conditions."
It was important to the agency that, as tangata whenua, Ngā Hapū o Ōtaki decided tikanga with regards to the discovery, he said.
"This protocol has been developed alongside ngā hapū to ensure correct cultural processes are followed when accidental discoveries like this are made.
"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.