Work on the Huntly section of the Waikato Expressway unearthed a human skull today, which appears to have been buried in a kumara pit.
Archaeologist Collin Sutherland said it was "one in a thousand" to find remains in a kumara storage pit.
"It's a skull, it's more than likely koiwi or human remains," Mr Collins said.
"It's fairly rare to find human remains in a kumara pit but it's not unheard of. Most often you get the reaction that it's counterintuitive to have the dead associated with food."
From first impressions Mr Collins said it seemed the skull was placed in the pit late in its creation.
"Who knows how it got in there? It seems to have gone in fairly late in the piece. The kumara pit has been filled up and maybe it slumped a little, then the skull has gone in."
Archaeologists have been on the site for two days and at this early stage of the excavation it appears that the skull has been broken in two, but Mr Sutherland was not ruling out the possibility of the separate fragment belonging to a second skull.
The distance between the two pieces led Mr Sutherland to theorise that it was likely the skull had broken when it was placed into the pit.
He said the area around the skull would be carbon dated to give an indication of the age of the remains and that it was most likely pre-European.
Waikato-Tainui project manager Moko Tauariki said when the remains were fully excavated they would be sent to Auckland, where they would remain for a week of analysis before being returned for reinterment at Taupiri Mountain.
With a pa just north of the site Mr Tauariki said he had his own theories of the reason for the skull being found in the pit.
"It's hard to say, when the British came through they never came through peacefully. It could possibly be that they killed the people of this area. We know this is a sacred site. It is interesting that there is a head there but no other parts of the body that we can see at this stage," he said.
"We could theorise on lots of different things, but I can just theorise they were probably ambushed and didn't know what hit them, and then just left."
He said kumara pits were never used for burials.
The kaitiaki, or guardian, of the site Kawe Nikora said her main purpose on the site was to protect the environment.
"We look after the fish and the birds and especially the bones that are found. We try and protect them and relocate them away from the Expressway.
"Is our job important? Yes it is when you think of the history and the Maori Wars. The second king said 'once the land was taken, it should be returned'. What we are saying here is that what happened in the past has happened but we are now here to make sure no more damage is done to the area and everything is safe."
She said if they found one set of remains there would be others around.
"We will continue here throughout the whole project... I need people to know the importance of having a kaitiaki ... It's really important that we protect our land."
Ms Nikora said she wanted media to take images of the skull in order for people to know about the find.
"You cannot close everything off and hide it. Everyone needs to know," she said.
The kumara pit can be identified by a rectangle of darker soil around the brighter native clay.
The pit is the largest of a number of similar pits on the site.
The site originally became of interest as a midden, or shell heap, which was discovered last Wednesday, with the kumara pit and koiwi discovered a few days later.
The site is located in an area between Ralph Rd and Lake Kimihia.
Land Transport Agency's Hamilton highway manager Kaye Clark said project protocols which NZTA had developed alongside Waikato-Tainui immediately came into play when the remains were uncovered.
"Our protocols include provisions for kaitiaki to work on site, as needed, to monitor earthworks as they unfold. This discovery was made by the kaitiaki and the project archaeologists working alongside each other, which is exactly what should happen," she said.