The FDA is saying that parents and doctors should not give ingestible fluoride tablets to children under three years old.
Doctors may prescribe the tablets to youngsters who have no fluoride in their drinking water, saying that the absence of this mineral, which can strengthen teeth, raises the risk of tooth decay and cavities.
But the tablets have never been approved by the FDA and differ from toothpaste and mouthwash because they are swallowed.
In its announcement released Friday, the agency said it had sent notices to four unnamed companies that make the tablets outlining its intention to take action.
It also warned that their products should carry labels limiting their use to children at high risk of tooth decay, or those with poor dental hygiene.
In a scientific evaluation published today, the FDA said it had concluded that ingestible fluoride tablets should not be used in children under three or by older children who are not at high risk of tooth decay.
Revealing the announcement, Health and Human Services Secretary Robert F Kennedy Jr told Daily Mail: 'This Halloween, the FDA is driving a stake through the heart of outdated science and protecting our kids from the risks associated with ingestible fluoride.
'It's scary that these products have been used for decades without safety approval. Today's action raises public awareness, informs medical professionals, and builds on President Trump's commitment to Make Our Children Healthy Again.'
The action came after a review of scientific evidence, the agency said, which suggested that, for the same reason fluoride kills bacteria on teeth, it also harms the microbiome, or bacteria community in the gut, which may have 'broader implications'.
It also referenced a Cochrane Review, the gold standard for scientific evidence, which found no clear evidence that the supplements reduced the risk of tooth decay in primary, or baby, teeth, which children typically have until the ages of six to 12 years. The FDA did not cite the review, although it appears to be referring to a 2011 report.
The agency also referenced a bombshell federal report released last year, which suggested that exposure to fluoride in drinking water could lower IQ by up to five points.
It is the latest move by the administration to tackle the use of fluoride in the US, which has become a mainstay in drinking water after the substance was shown to strengthen teeth and reduce the risk of cavities.
Many US states have been adding fluoride to their drinking water since the 1950s in what was long been considered one of the greatest public health achievements of the 20th century.
Estimates suggest that fluoridation, the addition of fluoride to public water, saves $6.5billion in dental treatment costs every year and reduces the occurrence of cavities by up to 25 percent, according to the CDC.
But RFK Jr has slammed fluoride as an 'industrial waste', saying in November last year that it had been linked to arthritis, bone fractures, bone cancer, IQ loss, thyroid disease and neurodevelopmental disorders.
The Health and Human Services Secretary, who is a former environmental lawyer, said in May that ending the use of ingestible fluoride in the US was 'long overdue'.
He has made ending the use of fluoride a cornerstone of his Make America Healthy Again agenda.
Dr Marty Makary, FDA commissioner, said today in the agency's release: 'There are better ways to protect children's teeth than taking unapproved ingestible fluoride, which is now recognized to alter the gut microbiome.
'The microbiome is increasingly recognized to be central to a child's health and development.'
The agency revealed in May this year that it had begun the process of banning prescription fluoride tablets for children, and would reveal its decision in October.
Today's release is an update on this process, and comes after the agency spent months gathering and evaluating scientific studies and engaging with parents, clinicians, advocates and other stakeholders.
Ingestible fluoride has been in use in the US for decades, although it is unclear how many children use it.
The American Dental Association has railed against plans to ban the tablets, saying there is no evidence they cause harm.
In a release in May, it said the tablets were effective at reducing tooth decay.
It also slammed research linking fluoride and changes in the microbiome as 'limited' and raised concerns that reducing the use of the tablets would raise the rates of dental cavities.
Dr Brett Kessler, a dentist and its president, said at the time: 'Proposals like this stand to hurt rural America, not make them healthier.
'More than ever, at this critical time in American health care policy, it is vital that we slow down to properly study the full implications of actions like this on the health of the nation.'
He added: 'In non-fluoridated communities, especially rural areas, fluoride supplements are the only chance for individuals to get the appropriate amount of fluoride to prevent tooth decay.'
Dentists say that everyone should brush their teeth at least twice a day, ideally in the morning and evening, to remove plaque and bacteria that can lead to cavities and gum disease.
But estimates suggest that about 30 percent of Americans do not do this, raising their risk of tooth complications and bad breath.
Dentists have previously said that it is best to reinforce teeth brushing from a young age so that it becomes a habit that is carried forward into adulthood.