He said layers of charcoal about 25cm below the top sand layer indicated the presence of umu (Maori earth ovens), which had been used to cook moa.
The first scientific dig in the South Island, in 1852 , unearthed moa bones on the same site.
"This is a very important site, both in it's own right and historically."
Doc Otago's historic technical adviser Shar Briden said although it was rare for the department to actively be involved in excavations, this was a special case.
"We try not to do excavations and disturb a site unless it is a dire emergency."
Ms Briden said the Awamoa Creek dig was a rescue excavation, and archaeologists at times had needed to work in thigh-high water to rescue as much as they could before the tide came in.
"It is definitely archaeology on the edge."
The dig would conclude today, and the artefacts sent to Otago and Canterbury universities for further analysis, she said.