Chief executive Alex Parmley said the Thames St council headquarters was secured from about 3pm after a conversation between a member of the public and council staff escalated into "a threat" of physical violence.
The caller had indicated they would come to the council office to carry out their threat.
"There was a communication with one of our staff by a member of the community who we were dealing with which posed a threat to staff.
"We took the threat seriously and reported it to police, and took the precaution of locking down the headquarters for less than an hour whilst police followed up with the person."
Mr Parmley said the threat applied to the main headquarters.
Other council offices scattered along Thames St, including the Oamaru Public Library, remained open during the incident, which ended about 3.50pm.
Mr Parmley said it was lifted once local police "clarified" the person who had called the council was "not considered a threat".
Police in Oamaru said this evening the details of the alleged offender were not immediately available.
Waitaki Mayor Gary Kircher said he was appalled at the alleged behaviour of the male caller.
Mr Kircher said while there had been "occasional threats" to council staff, where members of the public boiled over, threats of violence could never be justified.
"In some ways it’s just getting way too carried away in their feelings about a particular issue.
"That type of behaviour by anyone is totally ridiculous.
"I understand the police have spoken to him and I understand he is pretty embarrassed. It’s just not acceptable."
However Mr Kircher said what had happened was a "rare" incident.
It was a far cry from the late 1990s when the council office was firebombed over the Oamaru Aquatic Centre build, "which shocked people given the extreme nature of it".
"There’s been occasional threats.
"Safety of our staff is really important, and if people have got a problem I think we give them every opportunity to talk about it.
"I certainly like to think we give people the opportunity to deal with (issues)."
Mr Kircher said there seemed to be "a lot of pressure on a lot of people" at this point in the electoral cycle.
That included residents expressing worry about the role of the council and its impact on the community.
"I absolutely feel for all those (people). Some of that pressure comes from council.
"We are required to do things. There are things we don’t necessarily like doing — some aspects of the District Plan we are required to do them and there are other things that people just disagree with.
That’s fine — that’s democracy — but to go to these lengths is unacceptable," Mr Kircher said.
Mr Parmley said the incident was the first in his three-and-a-half years at the helm.
"We had to take it seriously. We have a procedure for dealing with these situations.
"If we feel there is a credible threat, we go into lock-down."
Mr Parmley said it was unfortunately increasingly a feature nationally for councils.
"Luckily these threats are very rare. Certainly my first in my time here we’ve had to go into lock down."
The staff involved in the threatening phone call were being supported.
