The recommendation comes on the heels of a recent statement from the American Dental Association that also asks parents not to mix infant formula with fluoridated water because of the risk it poses to the children.
It is the strongest statement to date from either the ADA or the health department concerning the health risks of the compound that is added to many municipal water supplies in the country to battle tooth decay.
"This warning went out to every dentist and pediatrician in the state," said Steve Arthur, oral health director for the Department of Health. "We now know that when dealing with infants that less is best."
The health department, and the ADA, still strongly endorse the use of fluoride in public water supplies and the groups also encourage people who do not get fluoride from their water to take daily supplements.
But recent research has proved that babies who are getting most of their nourishment from powdered formula take in much more fluoride, per weight, than older children.
The new studies show that high levels of fluoride in infants can cause discoloration of the teeth known as fluorosis.
The American Academy of Pediatrics recommends breast feeding exclusively for the first six months, the health department said in a press release.
Arthur said prior to the new recommendation both the ADA and the Vermont Department of Health warned that parents should probably be aware of the amount of fluoride given to young children.
Arthur called fluorosis a minor health problem and he said the warning was given out to let parents know about the risk.
"This corrects a contrasting and confusing recommendation," Arthur said. "We are saying that we now have this information and we want to get it out so parents can make the choice."
Water has natural levels of fluoride, and Arthur said that parents should have their water tested if they use well water to mix formula.
The battle over adding fluoride to public water has raged across the state over the past few years.
In 2001, Brattleboro residents voted not to add the chemical to the town's water.
Last year voters in Bellows Falls rejected a proposal that would have stopped the use of fluoride. Bellows Falls adds fluoride to its water.
Burlington also recently decided to continue adding fluoride to the city's water.
Peter Taylor, executive director of the Vermont State Dental Society, said that even with last month's ADA statement and the more recent Vermont Department of Health warning, most dentists in the state still support water fluoridation.
"The ADA said there was a small possibility of fluorosis in infants and it is important that parents know about that," Taylor said. "Community water fluoridation is still good public health policy."
But Michael Connett, an anti-fluoride activist who works for the Fluoride Action Network, said the health department warning is an important wake-up call and should not be taken lightly.
For years, Connett said, both the ADA and the Vermont Health Department have been hesitant to do anything but fully endorse the use of fluoride.
A recent article in the British medical journal, The Lancet, reported that fluoride may also damage a child's developing brain.
And on Oct. 14, the U.S. Food and Drug Administration notified bottled water manufacturers that they can not claim that fluoridated water that is marketed to infants prevents tooth decay.
Adding fluoride to public water forces users to ingest the chemical whether they want it or not, Connett said. He called the practice reckless.
"It took them 60 years to finally acknowledge that fluoride is dangerous for infants," said Connett. "If fluoride is not safe for everybody than it is not safe for anyone. Period."