The Supreme Court has ruled that a council can add fluoride to the water supply in South Taranaki, despite legislation stating people have the right to refuse medical treatment.

The court made a majority decision that adding fluoride to drinking water did fall under section 11 of the NZ Bill of Rights Act, which gives people the right to refuse medical treatment, but it ruled the council's power to add the fluoride was a "justified limit" on that right.

South Taranaki District Council was given the go-ahead to fluoridate water in Waverley and Patea after a Court of Appeal ruling in 2016.

The Court of Appeal rejected anti-fluoride group New Health New Zealand's argument that fluoridation of water amounted to medical treatment, which the public should have the right to refuse. But the group challenged that decision. Lawyer Mary Scholtens QC, said at a hearing in the Supreme Court in November last year that fluoridation was adding a substance to drinking water for a therapeutic medical purpose, which had a medical effect and therefore qualified as medical treatment.

She said adding fluoride breached section 11 of the Bill of Rights Act, which states everyone has the right to refuse to undergo medical treatment.

She also argued the council was not legally authorised to add fluoride to the water.

But the Supreme Court disagreed.

It dismissed the appeals and awarded costs of $20,000 to the council.

Today's ruling follows a six-year legal battle that began when the lobby group took the matter to the High Court, where the council's right to fluoridate the supply was also upheld. The Ministry of Health then declared fluoride was not a medicine, after the High Court recommended it consider passing a regulation under the Health Act to put the matter beyond doubt.

South Taranaki mayor Ross Dunlop said the legal battle had cost the council at least $300,000-$350,000, though the Ministry of Health had assisted with funding.

"We had a request from our local district health board to add fluoride into some extra communities in our district. We took that up, not expecting to end up in a very complicated legal situation," he said.

"We were just trying to do the right thing, particularly for young people in our communities with challenges in oral health. It turned into a major legal battle, which wasn't our intention."

Water New Zealand chief executive John Pfahlert earlier said the benefits of fluoride protection for dental health were "irrefutable".

He said fluoride posed no health risks at the recommended levels of 0.7 to 1.0 parts per million in drinking water.

Anti-fluoride campaigner Mary Byrne said outside court this morning she was disappointed with the ruling.

"We think it's really disappointing and we think it defies logic," she said.

"If you go to the pharmacy and you buy fluoride tablets it has directions and dosage and it has warnings ... fluoride is a medicine."

She said fluoride was shown to lower IQ.