More than 70,000 Aucklanders left their district health board (DHB) voting pages blank or voted incorrectly in recent local body elections.
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Electoral officials said that mirrored voter apathy about health boards around the country, though figures for other regions were not yet available.
The revelation is prompting calls for the system to be overhauled, given DHBs control billions of dollars between them.
However, Health Minister Jonathan Coleman said he had no plans to review how DHB members are decided.
Just 38 percent of Aucklanders voted in council elections, but even fewer were motivated to elect their health boards.
Preliminary figures showed 55,000 returned their papers with the DHB section completely blank.
Another 17,000 forms were unusable because they were not filled out correctly.
Long time health campaigner Sandra Coney, who has just been elected to her third term on Waitemata DHB, said the voting system was confusing.
Part of the problem could be that people had to tick the ballot for mayors and councillors, but then rank DHB candidates by number as part of the STV system, she said.
"I myself ticked the box when I got to the DHB members and then realised I'd done the wrong thing, and I had to ring up - I was going to get a new set of papers but they said if I whited out my tick and then put the number over the top of it, I would be all right."
The system was not fair on people trying to make their voice heard, Ms Coney said.
"Our voting numbers are low enough without losing votes.
"People who do vote go to the effort to do it, and it must be disappointing for them if they realise afterwards that they've done the wrong thing."
Labour Party health spokesperson Annette King said something was wrong and it was time to look at whether to change the voting system.
"Health is one of the big issues of importance to New Zealanders - how the money is being spent, what are the services that are being provided.
"It's an important democratic vote people have to elect men and women who are competent and capable of making those decisions."
Most DHBs have seven members elected and four appointed by the government.
But New Zealand Institute of Directors president Michael Stiassny said it was time to consider whether there should be more appointed representatives, to ensure there were qualified and motivated people on the boards.
"We have more than the majority of Aucklanders - or New Zealanders, actually - saying, 'We don't care who's appointed' - that's an issue."
But Health Minister Jonathan Coleman said he was not considering a change to the elected and appointed ratio, and also had no plans to review the voting system.
However, he conceded the process was flawed.
"By the time [voters] get to the DHBs, they've spent quite a bit of time on this exercise and then they're often confronted with a long list of people whom it's difficult to sort out, and then they're having to jump to another voting system - so yeah, it's not the most ideal process, that's for sure."