The Health Ministry is appealing a High Court decision that found its order forcing 14 councils to fluoridate was unlawful.
Some councils have paused their plans to fluoridate town supplies, while they wait for the legal matters to be sorted.
The High Court found in November that former Director General of Health Ashley Bloomfield did not adequately consider the Bill of Rights Act regarding the right to refuse medical treatment, when he told 14 councils they had to fluoridate drinking water.
The Ministry promptly wrote to the councils, telling them to keep going with fluoridation because the decision did not quash the directive, it simply referred to a process error.
The current director general Diana Sarfati and attorney general Judith Collins have now lodged an appeal in the Court of Appeal.
Separately, their legal teams were back in the High Court on 2 February with the anti-fluoridation group that brought the review, New Health New Zealand, because the two sides could not reach an agreement on how to move forward after the November decision.
The legal action left some councils feeling in limbo.
Rotorua mayor Tania Tapsell said all fluoridation work there was on hold.
"Following the High Court ruling on this last year we paused implementation and sought further guidance and legal clarification from the director general of health about how to proceed with the government's directive to fluoridate. We are still waiting on this," she said.
Horowhenua had also put everything on hold, saying it was in a difficult position between the court decision and the push from the Ministry to still continue.
The Whangarei and Waitaki councils were continuing to build the equipment needed to fluoridate, but said they did not plan to add fluoride to drinking water until there was more legal clarity.
Whangarei mayor Vince Cocurullo said his council planned to survey residents.
"As mayor I do get phone calls or emails [from] people who are for fluoridation and people who are against fluoridation - so there is both sides of the coin. What we just try to do is make sure their voices are heard," he said.
Nine of the 10 other councils contacted by RNZ were following the Ministry advice that the order to fluoridate stood, and were proceeding. One did not respond.
Some said they feared fines if they missed their deadlines, which differed.
The Ministry of Health was given responsibility for making decisions on water fluoridation in a law change in 2021, when previously it had been left to individual councils.
The other councils which have been directed to fluoridate are Kawerau, Hastings, New Plymouth, Waipa, Nelson, Far North, Auckland, Tararua, Tauranga and Western Bay of Plenty.