The Electoral Commission said it received 1,527,042 votes, which included 148,022 informal votes (9.7 per cent) and 2476 invalid votes (0.16 per cent).
The voter turnout was 48.16 per cent of registered voters.
The flag, designed by Kyle Lockwood, won in the fourth round of voting, taking 50.53 per cent of the vote.
The next most preferred flag design was Lockwood's red, white and blue flag, which polled 49.47 per cent.
It was followed by Red Peak, the black and white silver fern, and the koru.
A final result in the narrowly-fought contest will be announced on Tuesday, once late votes and overseas ballot papers have been counted.
The margin of victory is so small that the final result could change.
In the first round of voting, Mr Lockwood's red-coloured flag received the most votes.
But it failed to get a clear 50 per cent majority. That meant the Andrew Fyfe-designed Koru was eliminated from voting as the lowest-ranked flag.
The Silver Fern (Black and White) was the second flag to be eliminated, followed by Red Peak.
The relatively high proportion of informal votes - 9.7 per cent - was likely to be the result of protest votes from people who did not want a change of flag.
Anyone who spoiled their ballot paper or refused to give clear instruction had their ballot paper counted as an informal vote.
The preliminary turnout was 48.16 of the voting population - higher than the last postal referendum but relatively low for a constitutional issue.
The Government expected much greater voting numbers in the second referendum, which will be held in March.
Labour leader Andrew Little said the alternative flag was always likely to have a silver fern on it given the final five options.
"The informals were nearly 10 per cent, which was a very high proportion, and the fact that there will be some people who voted for the other flags who won't like the blue and black design, plus the fact that it was still under 50 per cent return, suggests we are on track to have no change to our flag.
"And I think people will rightly ask what have we got for $26 million."
Mr Little would not say how he voted, but said he did not vote for the Mr Lockwood's blue and black silver fern.
Deputy Prime Minister Bill English, the minister responsible for the flag consultation process, said the results showed strong public interest.
"While this is a preliminary result, New Zealanders can now turn their attention to deciding whether to keep the current flag, or replace it," Mr English said.
"We'll know definitively once the Electoral Commission announces the official result on 15 December."
Returned and Services' Association (RSA) national president BJ Clark said he was still confident the current flag would be retained despite the selection of Kyle Lockwood's blue and black silver fern flag.
"It doesn't change anything for us. A flag obviously was going to be selected so now we can get on with leading up to the second referendum.
"It didn't matter which flag was selected, obviously, that was just going to be one that is going to be put up against the current flag," Mr Clark said.
"We are still receiving a lot of support for the RSA to continue fighting for the current flag."
Mr Clark said, if anything, the flag selection had "reinvigorated" New Zealanders' passion for the current flag.
"Interestingly, if there can be a positive out of this, I was just driving the other day from Wellington to Dannevirke and was surprised at the number of New Zealand flags, the current flags, that are being flown. When you look around I think now more and more New Zealand flags ... are being flown."
Mr Clark said it was now a simple choice for New Zealanders between the preferred option selected tonight and our current flag.
He encouraged New Zealanders who supported the current flag to fly it wherever they could.
"Not everyone has a flagpole so people can also fly the flag by getting a flag bumper sticker from the RSA and posting a virtual flag on social media."
