Mrs Duncan said there were likely to be many skeletons buried in the dunes along the coast.
"The whole costal dune is littered with graves. They are not marked or anything. It extends from over about 300 years where there was a battle between neighbouring tribes of Te Aroha, Ngai te Rangi and Nga Potiki. Where they were killed was where they were buried," she said. "It is common [to find them during construction] and they are probably still underneath the sand out there."
Once the bones had been analysed they will be returned to Nga Potiki and buried at an ancient burial ground at the end of Maranui Rd.
Heritage New Zealand regional archaeologist Dr Rachel Darmody could not say how much of the skeleton was buried together as it was still being uncovered.
It was not unusual to uncover a skull in Papamoa but it was a bit more unusual to find a full burial, she said.
She confirmed it was historic human remains but said it was too early to say exactly how old it was.
Police Detective Senior Sergeant Greg Turner said finding a human skull in the Tauranga and Mount Maunganui area was not uncommon.
"Tauranga has significant burial areas pre-dating European settlement."
Skulls would be found in the area about three times a year, he said.