The move was taken to avoid any perceived conflict of interest, health officials said.
Some parts of England have agreed to add fluoride to the water to prevent tooth decay in children and the north west is preparing for a consultation.
Mr Burnham is MP for Leigh. A spokeswoman for the Department of Health said: "Andy Burnham has held an honorary position with the British Fluoridation Society as vice president since 2004.
"Following his appointment as Secretary of State for Health he will be relinquishing this position as he appreciates that there could be a perceived conflict of interest.
Effective
"We believe that fluoridation is a scientifically supported and effective means of addressing health inequalities by reducing tooth decay in children and adults, especially those from poorer backgrounds.
"There is no question of central government imposing fluoridation. Decisions should be taken locally following consultations conducted in accordance with procedures approved by Parliament in 2005.
"The consultations should cover the benefits of fluoridation, any possible risks to health and the ethical arguments for and against a population based approach to improving health."
Southampton decided to bring in fluoridation earlier this year but that decision is subject to a legal review. In the north east and West Midlands, fluoride has been added to water since the 1980s. Tweet
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Flouride is a poison. If I want to eat chemicals I will do but to force feed the masses with it is a disgrace. Tooth decay does not harden the arteries but flouride does. Tooth decay will come down but the incidence of heart attacks will sore. Maybe it's a ploy to relieve stress on the NHS. Bump off the oldies and all the kids will have shiny teeth. "Eat your chips and drink your coke Chantelle". Nuff Said.
The American Dental Association advises that infants are not given formula feed made with fluoridated water. Why are our Health Advisors not issuing the same advice?
Why are they mass medicating the whole population with a toxic chemical in an approach that ignores all precautionary principles?
Why don't we follow the example set by Scotland and provide better dental education and provision...tackling the holistic problems of nutrition, hygiene and general health?
http://www2.fluoridealert.org/Alert/United-Kingdom/Scotland/Children-s-tooth-decay-on-decline-in-unfluoridated-Scotland
Levels of tooth decay among primary one pupils in Scotland are falling, according to new figures.
The statistics indicate that tooth brushing schemes and education programmes in Scotland's nurseries and primary schools were working.