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The revelation has prompted Cr Richard Thomson to call for a policy rethink, while Public Health South medical officer of health Dr Marion Poore warned, over time, it was possible more tooth decay could result.
''This means that the benefits of fluoridated water supply to the whole community are reduced,'' she said.
The council voted in May last year to reduce the amount of fluoride being added to the city's drinking water from 0.85mg per litre to 0.75mg per litre. The council had previously targeted 0.85mg per litre to ensure the dose administered fell within ministry guidelines, which recommended a range between 0.7mg per litre and 1mg per litre to protect against tooth decay.
However, council water production manager Gerard McCombie warned councillors at the time the change to the lower target could result in the actual dose dropping below the ministry's guidelines. That was because of inaccuracies in the delivery mechanism which meant the actual dose administered fluctuated each time, he said.
A majority of councillors voted to proceed anyway, urged on by Cr Kate Wilson, who suggested the change, and the switch to a lower dose was made days later.
Since then, the actual dose being administered had dropped below ministry guidelines 65 times, data released to the Otago Daily Times following an official information request showed.
That compared with just five misses in the first half of the year, before the change to a lower target was made.
Mr McCombie told the ODT trying to hit the lower target, rather than fall within the range, was ''a bit like trying to hit the bullseye with every dart''.
''Sometimes, we're a bit above it, but quite a bit of the time we are below it,'' he said.
As a result, council staff were reviewing the entire dose system to try to improve accuracy, although absolute accuracy would be ''impossible to guarantee'', he said.
Cr Wilson defended the decision to lower the dose, saying councillors wanted to set it, rather than leave it up to staff.
They also wanted to take a ''conservative'' approach, given public concern, including about the health of infants consuming fluoridated water with powdered baby formula, she said.
She was also surprised council staff had not reported the problem to councillors, or adjusted their sights.
''I'm not quite sure why it is so flexible. I think if you're targeting 0.75 and you're finding you're getting a whole lot of readings below 0.7, then you should be aiming higher.
''That's what the idea of a target is.''
However, she conceded regularly missing the target was ''something we may need to address''.
''If we're not hitting that, I'm very happy to open the debate again.''
Cr Thomson - also a Southern District Health Board member - said the decision to lower the dose had been made ''on the hoof'', and the council now needed to rethink its approach.
He did not know if the repeated misses - sometimes for more than a week on end - raised public health concerns, but said that was the ''fundamental question''.
''Does it matter? And, if it does, then in my view, we need to have another look at it.''
Fluoride was added to 85% of the city's drinking water - at the Mt Grand and Southern water treatment plants - and had been credited by health authorities with reducing levels of tooth decay.
However, opponents have mounted repeated campaigns to end ''mass medication'', citing a variety of health concerns. The council received 34 public submissions on fluoride at its last annual plan budget hearing, the most on a single subject.
Dr Poore said the ministry's recommendations aimed to reduce tooth decay for the whole community.
''Tooth decay is the most common chronic disease in our community and causes misery ... loss of a smile, painful infections, requirement for dental procedures, time off work and school.
''It makes sense to add fluoride to community water supplies in a way that the recommended levels are reached consistently - do it properly to get the most benefit,'' she said.
However, she acknowledged there could be ''challenges'' maintaining exact levels.