But the issue would be open to public consultation through the strategy and policy committee, which has assumed responsibility for the debate.
An amendment to the motion by councillor Dave Macpherson, to stop fluoridating Hamilton water by July 1, was dropped.
Deputy Mayor Gordon Chesterman and councillor Peter Bos spoke against axeing the referendum.
"It goes, for me, against democracy," Mr Bos said. "If we do what is the will of the people, then why not go back and ask those people what they want?"
Mr Chesterman said he was concerned about the process, which had included a large discussion on fluoride 14 months ago.
"We've made a collective decision to have a referendum so I will be voting against the motion to remove the referendum and refer it to the committee.
"I see this as a backdoor method of making the decision to remove fluoride."
Councillor Maria Westphal said the process needed to be clear and democratic and the best place for that to happen was at committee level.
Hamilton City Council began adding artificial fluoride to its water supply in 1966 to fight tooth decay and improve dental health.
It costs $40,000 a year but is thought to save more than $1 million in dental care costs.
A $160,000 referendum in 2006 drew only t 38 per cent of voters, and 70 per cent of these voted to keep fluoridation.
Waikato District Health Board chief medical officer of health Dr Felicity Dumble has previously said there was no risk of fluorosis (discoloured teeth through under-developed enamel), osteosarcoma (bone cancer), brittle bones or lower IQs in children if fluoride was used at recommended levels, which in New Zealand was between 0.7mg and 1mg per litre of water.
In Hamilton fluoride is concentrated at 0.7 parts per million, a "top-up" to the naturally occurring fluoride already in the water.
Anti-fluoride lobbyists say it affects the absorption of folic acid, causes anaemia in pregnancy and led to more pre-term deliveries, interfered with the thyroid and affected fertility.
Hamilton City Council last year received 120 submissions to its annual plan on the topic. They followed a presentation to the council in April by US professor Paul Connett, who likened fluoride to an industrial grade waste product.
