The trust and the council have clashed publicly over the heritage aspects of several planned city developments since the beginning of the year.
Matters came to a head last month when the trust took the rare step of prosecuting the council for alleged breaches of an archaeological authority issued for the Wall St retail development in George St.
Tensions between the two organisations have escalated since the arrival of a new trust Otago-Southland area manager, Owen Graham, in August last year.
Mr Graham said this week while the trust "was not here to annoy people", it was here to reinforce its statutory role to protect and preserve the historical and cultural heritage of New Zealand.
A nationwide restructuring of the organisation completed last year and the addition of more staff in the Otago-Southland office meant the trust now had the resources and capabilities to do that.
While "many good things had happened in Dunedin," consideration of heritage issues "had slipped a bit", he said.
"We are putting it back on the agenda as a legitimate item for consideration."
Much of Dunedin's image was built on its heritage, he said.
"We keep hearing what a fantastic city this is because there is so much of its heritage left. We are trying to get people to keep us in the loop early [on developments involving heritage sites]. If we are involved early we've then got a chance to influence the direction."
Asked if the trust was targeting the council for special attention, Mr Graham replied it was not.
However, he said the trust concentrated more on local authorities than private property owners.
The Dunedin City Council should be leading the way on heritage matters, he said.
"If the city does things right, others will follow."
Mr Graham would not give details of the Wall St prosecution because the matter was before the courts. But he said the decision to prosecute had been taken after careful consideration by the trust's legal team in Wellington.
"It [the prosecution] didn't just happen over one thing."
