The Dental Council "accepted that the comments were made in good faith in a challenging interview situation and that there was no deliberate attempt to mislead the public".
In the letter from the council, addressed to Hawke's Bay naturopath and anti-fluoride campaigner Kevin Tinker, the council said Beaglehole "rigorously rejected" the suggestion he lied or violated professional standards.
The council recommended Beaglehole seek media training and said he was cautioned about expressing his views in public on the subject of community water fluoridation.
The campaigners have called the council's response "woefully inadequate".
Anti-fluoride spokeswoman Mary Byrne said Beaglehole's comments were misleading because there was "virtually no water fluoridation in the whole of Europe".
In 2014, a panel commissioned by the Prime Minister's Chief Science Adviser Sir Peter Gluckman and the Royal Society of New Zealand president Sir David Skegg found there were "no adverse effects" of fluoridation of public water supplies.
A Dental Council spokeswoman said the letter was not publicly released, as stated by Fluoride Free New Zealand.
Beaglehole is overseas and unavailable to comment.
The NZ Dental Association said: "Dr Beaglehole is a leading advocate and spokesperson for sensible, safe, proven and effective actions leading to the improvement of dental health of our communities; community water fluoridation and reduction of sugar consumption being very high on his and the Association's list of effective measures to reduce tooth decay.
"Dr Beaglehole is currently in Geneva for three months working with the World Health Organisation on issues regarding the reduction of sugar consumption."