The country's electoral commission said 56.61% of voters backed the existing flag, while 43.16% favoured a change.
Read more from our special coverage on "NEW ZEALAND"
The results are preliminary but the size of the margin means they are unlikely to change when the final tally is released next Wednesday.
The outcome will likely be viewed as a defeat for Prime Minister John Key, the main advocate for change, who described the existing banner as a colonial relic from the days of British rule.
"New Zealand has voted to retain our current flag. I encourage all NZers to use it, embrace it and, more importantly, be proud of it," he tweeted.
Deputy Prime Minister Bill English said some would be disappointed with the outcome but the government had staged a robust democratic process that had given people a choice.
The referendum was the culmination of an often-heated 18-month debate which touched on issues of national identity in the South Pacific nation of 4.5 million people.
On one side of the ballot was the existing flag, a dark blue ensign with the Union Jack in the top left corner and four red stars representing the Southern Cross constellation.
On the other was the proposed alternative -- a silver fern on a black-and-blue background, which retains the four stars.
Created by designer Kyle Lockwood, it beat four other proposed flags in a preliminary referendum last December.
Key called the existing flag a colonial throwback, saying the silver fern used by the All Blacks "screams New Zealand" in the same way the maple leaf identifies Canadians.
He described the vote as a once-in-a-generation chance to update the flag after more than a century.
However, veterans' group the Returned and Services Association argued that to change the flag disrespected previous generations who fought and died under the banner.
"We are delighted, but not surprised," it said after the result was announced.
Others criticised the new design's aesthetics, with "Jurassic Park" actor Sam Neill saying, "This ugly beach towel is no alternative. It's hideous."
But there were high-profile advocates for change, including ex-All Black skipper Richie McCaw, who said the existing flag was too similar to Australia's.
"The silver fern has always been the special symbol on the All Black jersey... So the new flag with a silver fern as a part of it would be a great option," he posted on Facebook earlier this month.
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