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The billboard, which said fluoridated water "lowers kids' IQs'', was not the sort of message the airport wanted outside its doors, a spokeswoman said.
However, the organisation that paid for it, Fluoride Free NZ, said it referred to a Canadian study it said was important and should be made known to New Zealanders.
The airport spokeswoman said the billboard, which was put in place over the weekend, "shouldn't have gone up''.
The airport used an advertising agency which owned the billboard infrastructure and sourced advertising, but yesterday the company was told to remove it.
The spokeswoman said the airport had both received a complaint and had its own concerns about the billboard.
It did not fit with the airport's "guidelines and values'' in terms of what advertising was allowed.
The issue was also "down to our values'', and how the airport worked with its business partners.
"We want to do what's right for the region and for our customers,'' the spokeswoman said.
She was concerned there was not enough information on the billboard to give a full picture of what was being claimed.
There had also been a call from a medical professional about the billboard, but by the time she spoke to that person there had already been discussions with advertising company Go Media about taking it down.
The airport had regulations in its lease agreement with the company, including that political advertising or alcohol advertising was not allowed.
In terms of the anti-fluoride advertisement, the company had "made a balls-up'', with a rigorous sign-off process not being adhered to.
Fluoride Free NZ spokeswoman Mary Byrne said her organisation had five billboards around the country.
She was not aware yesterday afternoon of the billboard being removed, but said a Canadian study it referred to was "a really important study''.
The study of 601 mother-child pairs, published in Jama Pediatrics, showed maternal exposure to higher levels of fluoride during pregnancy was associated with lower IQ scores in children aged 3 to 4 years.
It said in its conclusion the findings indicated a "possible need to reduce fluoride intake during pregnancy''.
Ms Byrne said it was the second United States government-funded study, and there had been others, showing fluoride was "neurotoxic''.
She said the organisation had not had billboards removed in the past, and would consider finding another spot in Dunedin.
The Southern District Health board was unable to comment on the issue yesterday, but promised to do so today.