Historic human bones have been unearthed on a new section of the Waikato expressway in Huntly.

The "koiwi", or pre-European, bones were found in a shell midden, or rubbish site uncovered by contractors laying culvert between Ralph Road and Lake Kimihia.

NZ Transport Agency said work stopped immediately at the site on the Huntly bypass section after the discovery of the skull on Tuesday afternoon.

GEORGE HEARD/FAIRFAX NZ The human remains that where found at a section of the Waikato Expressway that is under construction.

The agency implemented it's Koiwi Discovery Protocol and alerted Tainui iwi who conducted a blessing at the site at 6am on Wednesday, NZTA Hamilton Highway Manager Kaye Clark said.

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"This discovery was made by the kaitiaki and the project archaeologists working alongside each other, which is exactly what should happen."

Kaitiaki, or guardians, are based at the road works site to observe any areas of cultural significance under agreed protocol, she said.

Two sections of a skull, including the mouth and teeth, were uncovered in the pit dating back to pre-European settlements, Waikato Tainui Project Manager Moko Tauariki said.

"All we know is it is pre-European, into the late 1700s."

"We do know there was occupation here in pre-European time, and like most our history a lot of evidence has been built as the country has developed."

The remains would be lifted by an archeologist and sent to Auckland University to be examined by a physical anthropologist to determine the age, sex and possibly health of the person depending on the state of the remains, Project archaeologist, Dr Warren Gumbley said. Material around the site would be used to date the burial.

"It is an interesting site as the midden is shell midden, which would normally be found in more permanent coastal settlements. What we do know is they often used this shell inland in temporary settlements.

"We have also found a kumara pit at the site which suggests it may have been a temporary, seasonally occupied site, as opposed to a more permanent pa."

This was the first discovery of significance on the site of the new four lane bypass extending from Ohinewai to Ngaruawahia.

"We expect it along the expressway due to the land, as there are a lot of settlements here. We try to do a lot of work before excavate so we know the more likely sites where we will find things."

Clark said NZTA worked hard to align new highways away from any sites of significance.

"It's a very busy site with a lot of earthworks going around, at this stage contractors can go and work at other places on the site they have open. We are likely to be up and running within a few days."

Jocelyn Berryman, chair of the Tangata-Whenua working committee, said it was a historic moment.

"It is very humbling, my marae is over the hill, and my hapu here, it could be one of our family. It's great to be able to be involved and recognised."

Once the koiwi has been removed, examined and the site investigation was complete the koiwi will be reinterred at Taupiri Urupa by kaumatua.

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