In Taupo, 25,476 or 54.16 per cent of enrolled voters had their say while the numbers from the Waiariki electorate were much lower - 9285, or 26.21 per cent of enrolled voters.
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Nationally, 1,524,566 valid votes were received or 48.16 of enrolled voters.
Rotorua MP Todd McClay said he voted for the red silver fern design but would take some time to think hard before making his final choice.
"I sense a growing interest in the flag debate locally," he said.
He said he voted for the red silver fern design first with the black silver fern design second.
"The turnout was much better than for local body elections and I thought the national turnout was very good for a referendum.
"I will now take some time over the next few months and think about what the flag means to me. I'm likely to vote for change, but I want to talk to my family first."
Mr McClay said he expected to see a lot more people vote in the second referendum.
"It's hard to change an outcome after the fact if you don't vote," he said.
Rotorua mayor Steve Chadwick said she voted for the Red Peak design but would now vote for the status quo.
"I was always a Red Peak person. But I won't vote for change. The preferred design does nothing at all to excite me."