The Transport Agency said contractors found the bones, known as koiwi, when they were doing earthworks yesterday.
The area was blessed by Waikato-Tainui this morning and archaeologists have been working at the site to remove the remains and investigate the area.
The project archaeologist, Warren Gumbley, said the site contained a kumara pit, which suggests it may have been a temporary, seasonally occupied site.
The agency said it had had protocol planned since the start of the project with local Waikato-Tainui if koiwi were found.
