A study of 98 per cent of GP practices in England found that high rates of underactive thyroid were 30 per cent more likely in areas of the greatest fluoridation.
It could mean that up to 15,000 people are suffering needlessly from thyroid problems which can cause depression, weight gain, fatigue and aching muscles.
Last year Public Health England released a report saying fluoride was a ‘safe and effective’ way of improving dental health.
But new research from the University of Kent suggests that there is a spike in the number of cases of underactive thyroid in high fluoride areas such as the West Midlands and the North East of England.
Lead author Professor Stephen Peckham, Centre for Health Service Studies, said: “I think it is concerning for people living in those areas.
“The difference between the West Midlands, which fluoridates, and Manchester, which doesn’t was particularly striking. There were nearly double the number of cases in Manchester.
“Underactive thyroid is a particularly nasty thing to have and it can lead to other long term health problems. I do think councils need to think again about putting fluoride in the water. There are far safer ways to improve dental health.”
In England, around 10 per cent of the population (6 million) live in areas with a naturally or artificially fluoridated water supply of 1 mg fluoride per litre of drinking water.
The researchers compared areas to records from 7935 general practices covering around 95 per cent of the English population in 2012-2013.
Rates of high underactive thyroid were at least 30 per cent more likely in practices located in areas with fluoride levels in excess of 0.3 mg/l.
Fluoride is a naturally occurring mineral found in water in varying amounts, depending on the region and it is also found in certain foods and drinks, including tea and fish. It helps combat tooth decay by making enamel more resistant to bacteria.
But previous studies have found that it inhibits the production of iodine, which is essential for a healthy thyroid.
The thyroid gland, which is found in the neck, regulates the metabolism as well as many other systems in the body.
An underactive thyroid can lead to depression, weight gain, fatigue and aching muscles and affects 15 times more women than men, around 15 in 1,000 women.
The researchers say councils must rethink public health policy to fluoridate the water supply in a bid to protect the nation’s tooth health.
However Public Health England said that previous evidence overwhelmingly showed that fluoride in water was safe.
Dr Sandra White, Director of Dental Public Health at Public Health England, said: “Public Health England regularly reviews the evidence base for water fluoridation.
“The totality of evidence, accumulated over decades of research, tells us that water fluoridation is a safe and effective public health measure, and shows no association with reduced thyroid function.”
Other experts also warned that the study may have been skewed by population bias, a claim denied by the authors.
Prof David Coggon, Professor of Occupational and Environmental Medicine, University of Southampton, said: “It is quite possible that the observed association is a consequence of other ways in which the areas with higher fluoride differ from the rest of the country.
“There are substantially more rigorous epidemiological methods by which the research team could have tested their idea”
The research was published in the BMJs Journal of Epidemiology and Community Health.