Just over 43 percent voted for the alternative offering of a stylized silver fern with the Southern Cross on a blue and black field.
Voter turnout was 67.3 percent of the electorate, or more than 2.12 million voters, according to the Electoral Commission.
The result ends months of polarizing and sometimes bitter debate which has straddled political party lines.
Supporters of the prime minister, who openly supported the change, have described campaigners for the current flag as "immature" and politically motivated.
Key acknowledged the referendum result in a Twitter post, saying "New Zealand has voted to retain our current flag. I encourage all (New Zealanders) to use it, embrace it and, more importantly, be proud of it."
Deputy Prime Minister Bill English who was in charge of the process, said it had resulted in a "good debate around patriotism."
"We have run a robust, democratic process that has allowed us to discuss who we are and how we want to be represented on the world stage," English said in a statement.
"This process has engaged Kiwis in their homes, in their schools and in their workplaces, here in New Zealand, and right around the world --- it is something we`ve all had a point of view on."
The alternative option was selected by a Flag Consideration Panel that considered more than 10,000 flag designs submitted by the public and an initial referendum in which the public were asked to choose from a short list of five.
Final results will be released by the Electoral Commission on March 30.
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