Mr Clout said it was a "significant" find and the pa site was "central to the history of Tauranga Moana".
"There are likely to be significant remains found under the ground here. Pre-European pa settlement but also some early European artefacts are what we expect to find here.
"We're excited to explore this further."
Mr Kohu said Otamataha was one of four significant pa sites in Tauranga and was of great importance to local tangata whenua.
"The discovery of these trenches over here are a living museum for us."
According to archaeologist Ken Phillips' report for the council, in April of 1828 Hauraki tribes attacked and overwhelmed the Otamataha Pa.
The exact number killed or taken captive was not known but secondary sources estimated between 500 and 700.
Following the attack the Pa was abandoned as it had become tapu ground. However, it was unclear where the dead were buried following the attack.
"Numbering in the hundreds it is possible that they were not taken far and buried at Otamataha perhaps within an infilled defensive trench of the pa," Mr Phillips wrote in his report.