Mr Morris said the calls for vandalism were "feral behaviour".
"Some people suffer from this condition where anything the Prime Minister says or does, they get upset about it," he said.
"Like threats of burning down a flipping flag when there's a democratic referendum going on, what right do they have to say 'no you can't have that, we are going to burn it down'? It's just disgusting. What a bunch of punks. Who are they to say to me or anyone else 'no you can't see it'."
Mr Morris wanted to create a roster of volunteers to keep an eye on the alternative flag in the evenings to ensure it was safe.
"New Zealand is about more than a flag; it's about democracy and freedom of speech. The actions of a small minority of disgraceful vandals wanting to shut down debate dishonours what our soldiers fought for," Mr Morris said.
In 2011, the council came under scrutiny for flying a black flag on the flagpole in support of the All Blacks. Although the council owns the flagpole, after it was gifted to the city in 2008 by businessman Peter Farmer, it is subject to resource consent to fly anything other than the New Zealand national flag.
Mayor Stuart Crosby said the council had gone through the resource consent process before voting on the decision to fly it.
New Zealand First leader and former National MP for Tauranga Winston Peters said while he did not condone vandalism, he was extremely critical of the decision to fly the flag in Tauranga.
"We have one legal flag now, our national flag since 1902 and now you're going to have a flag up there with no legal authority whatsoever. That's ridiculous," Mr Peters said.
"For a council to decide to fly it because someone decided the flag pole was gifted to the city is flimsy in the extreme," Mr Peters said.
"I have no doubt at all the people of Tauranga will find this repugnant."
Tauranga Senior Sergeant Carl Purcell said any vandalism attempt on the flag would be unwise, given there were CCTV cameras in the area.
"If they were silly enough to do something to the flag they could be arrested and charged with wilful damage, which means they may appear in court but certainly it's a silly idea," Mr Purcell said.
"Should anyone think that it's a good idea, they do run the risk of being arrested and having charges laid against them."
Bill English, Minister of Flag Proceedings, declined to comment.
MP Todd Muller was surprised at the strong feedback against the alternate flag being flown.
"I find it very surprising that those supportive of the current flat, at times, seem to become very strenuous when there are efforts to allow the alternate flag to be flown for comparison.
"I think it's absolutely appropriate for people to see the two flags flying because then they can make a decision of which one they support."
He wondered why people were so vociferous in their opposition, saying "sometimes people get so focused on promoting their own perspective they forget the importance of allowing other voices to be heard as well."
Prime Minister John Key is in Australia and was unavailable for comment.
Last year New Zealanders were given a choice of four alternative flag designs to order in preference. The Kyle Lockwood-designed flag was the winning design and will now go up against the current New Zealand flag in a referendum next month. Several polls have found most New Zealanders do not support the proposed change.
Tauranga's official flagpole
•The flagpole is 27.6cm high.
•The current flag is 6m x 3m
•The project to erect it cost $100,00
•More than 10 sponsors joined the Tauranga Community Flagpole Trust.
•It costs more than $30,000 a year to maintain.
