Mayor Hamish McDouall said he was uneasy about a group of elected officials voting on the system that elected them.
"It's a bit like turkeys voting for Christmas or not."
He has had mixed feedback on the two systems from people and said there were pros and cons to both.
"I think we're making the right choice today," he said.
"This is an opportunity for people who support STV. STV has two years to go out and convince 6000 people rather than six elected officials.
"If they can't achieve that in two years then STV will lose what is a binding referendum."
Council has sought feedback over the past month and held a public meeting to discuss the two systems with the public.
Sixty-three per cent on 187 respondents to an informal online survey on the council website favoured retaining FPP.
At Wednesday's meeting councillor Josh Chandulal-Mackay, who supported STV, made a point of encouraging people to "stick to debating the substance of the issue".
"In the last month or so I've heard some really quite unattractive personal slights made against councillors who are in favour of FPP and equally those who are against," he said.
"I don't think there's any advantage whatsoever in people, for instance, putting out press releases calling councillors dinosaurs.
"And equally councillors criticising people of the public who have a different view."
Meanwhile, councillor Helen Craig said it was better to hold a referendum alongside an election rather than risking a public-initiated poll at a cost of $50,000.
"I know that we all have better uses for that money. I don't see that there's any urgency and it certainly doesn't warrant a poll right now."
Councillor Graeme Young said how STV worked was still misunderstood by many.
"There is significantly more education that has to take place before charging off down that path."
In May a 30-signature petition from "community leaders" asking council to change to STV was presented to councillors.
FPP vs STV
Under FPP candidates who receive the most votes are elected.
With STV, which is used in all district health board elections, voters rank candidates in order of preference.
As soon as a candidate has enough first-preference votes to be elected, their excess votes are transferred to voters' second preference and so on till enough people have been elected.