The apology comes after a review revealed the fluoride dosing facilities at water treatment plants in the region have been operating inconsistently because the machinery is getting old.
As the machinery could not be relied on, operators have been conservative with the amount of fluoride being put into the supply, Wellington Water documents said.
This is because there are health risks posed by high levels of fluoride, but it has also resulted in periods where dosage has fallen below the effective range.
This "monitoring and nursing" of the situation recently became "too onerous", the documents said. It was only at this point a review was commissioned.
Furthermore, as of last month, Upper Hutt, Porirua and Wellington City haven't been receiving fluoridated water at all due to operational health and safety concerns. The amount of work needed to fix the problem means residents could be without fluoride for nine months.
Associate Health Minister Dr Ayesha Verrall said it was "extremely disappointing".
"Fluoridation of drinking water is the most effective way to prevent tooth decay. Last year, as part of our Fluoridation of Drinking Water Amendment Bill, we passed legislation requiring those currently fluoridating their drinking water to continue to do so."
Wellington Water operates water treatment plants on behalf of Greater Wellington Regional Council and delivers the bulk drinking water supply to Lower Hutt, Upper Hutt, Porirua and Wellington cities.
Wellington Water Committee chairman Campbell Barry said questions will be asked as to why the inconsistent fluoridation went on for such a long period of time.
"It is unacceptable and we need to get to the bottom of it. It is disappointing and I think residents expect these things to be done properly in how we manage them.
"People can be assured there will be questions asked and there will be accountability and a plan moving forward to rectify it."
Barry said he was made aware at a high level of the long-term fluoridation issues about two weeks ago, but only found out on Tuesday that fluoridation had been stopped all together in some areas.
Greater Wellington Regional Council chairman Daran Ponter said he was also made aware of the situation earlier this week.
Ponter said he would have liked to have known about any issues earlier.
"Had this happened, we might have pulled the plug earlier as politicians and say actually these are our communities you're feeding this water to and we want this situation rectified now rather than in three or four years time."
Ponter said the council was sill trying to get answers as to why it was not told until yesterday.
"Certainly things hadn't been raised at a political level to suggest there was a problem of this sort of significance."
