The black and blue Southern Cross silver fern design got 50.53 percent of the votes in the first referendum, pipping the same design in blue and red on 49.47 percent.
The official result will be announced on Tuesday and will include votes NZ Post date-stamped before voting closed at 7pm yesterday.
The winner goes up against the existing flag in a second referendum in March next year.
The Electoral Commission sent out 3.1 million voting forms and 48.16 percent, 1.5 million were returned. There were 148,022 informal votes totalling 9.7 percent, and 2476 invalid votes totalling 0.16 percent.
Family First, a conservative lobby group, said there had been higher voter turnouts in citizens initiated referendums, which were not binding, but this Government-initiated referendum was automatically binding.
“This is a flaw with democracy in New Zealand when a stronger and more credible vote can be ignored simply because the Government didn’t initiate it,” says Bob McCoskrie, national director of Family First NZ.