On Friday, Macknight was alerted to a metre and a half of digging along the creek banks.
The site has been previously investigated under an archaeological authority granted by HNZPT to Te Rūnanga o Moeraki.
"The site forms part of important travelling routes for early Māori up and down the South Island, linking to coastal and inland networks," said Upoko Te Rūnanga o Moeraki David Higgins.
The area was the first archaeological excavation in the South Island.
"There is clear signage warning the public that this site is an archaeological reserve and not to remove items from the site.
"Under New Zealand law archaeological sites are protected and it is a criminal offence to modify or destroy the site without an authority," said Macknight.
Heritage New Zealand Pouhere Taonga, Waitaki District Council staff and Te Rūnanga o Moeraki are working together to assess the ongoing protection of the site, taking into account its proximity to an existing beach reserve, coastal erosion and its historical importance, she said,
• Anyone who may have knowledge about the recent site damage can contact Heritage New Zealand Pouhere Taonga on 03 4779871 or infodeepsouth@heritage.org.nz