Wanganui's water does not contain fluoride, and in a 2006 referendum 74 per cent of voters opposed its introduction.
Ms Main said "if" fluoride was beneficial for children's teeth, there were other ways to administer it, such as toothpaste.
"There must be a better way to more carefully target those at risk. If children are at risk ... then we live in a pretty creative country and I would have thought that we can come up with an acceptable and palatable way to do that."
She was unsure how a health board would be able to consult on the matter if given the responsibility.
"On a subject like that, there would be an expectation from the community that they would at least get to have a say." Even if such a policy was implemented, councils would still bear the cost because fluoride would have to be administered through council water supplies, she said.
Communities nationwide remain divided on whether to add fluoride to drinking water.
Hamilton residents voted overwhelmingly for fluoride last month after a heated debate saw the council remove it in July.
In Hastings a fluoride referendum was held alongside council elections last month, and residents voted to retain water fluoridation.
Anti-fluoridation group Fluoride Action Network has argued fluoride can be linked to adverse health effects such as arthritis, thyroid dysfunction, lowered IQ and hyper-sensitivity.
However the parliamentary health committee's report said scientific evidence was clear that adding fluoride to a town water supply in appropriate monitored doses led to a reduction of dental decay in children, particularly children living in low socio-economic families.
Health Minister Tony Ryall said fluoridation of public water was for local communities to decide.
Local Government New Zealand president Lawrence Yule said giving health boards the power to fluoridate would be a "huge shift". "It probably sits better there than it does with councils - we have no experience about the health risks, so I would probably welcome that overall."
