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However, the gap between those voting for and against the reform around cannabis shrunk 2.4% following the recount and addition of special votes.
Of the 2,908,071 total votes received, 48.4% supported the proposed cannabis legislation and control bill and 50.7% opposed.
The preliminary referendum results showed 46.1% voted for legalised cannabis, compared to 53.1% against.
It comes as the final results also show National has lost two seats, Labour has gained one, the Māori Party is back with two seats.
The incoming Government will still look to improve the current health-based approach to drug law reform.
Prime Minister Jacinda Ardern has said that some of the issues legalisation sought to address - including referring cannabis users to health services rather than the justice system - will be looked at regardless of the referendum result.
Auckland Central MP Chlöe Swarbrick, who cemented her seat today, says they always knew the results would be close and they are proud to have run "an evidence-based campaign for a harm-reduction approach".
"Despite the result, we're really glad to have sparked a conversation about the need for fit-for-purpose drug laws in New Zealand," Swarbrick says.
"As a country, we've come so far in understanding the need to reduce the harm of drugs by bringing them out of the shadows, and I remain committed to working for a drug harm reduction approach to drugs in the future."
Meanwhile, the final referendum results for supporting the End of Life Choice Bill is 65.1% (down 0.1%).
The final results - which include 504,625 special votes, or 17% of the total - will not change the parliamentary majority that Labour holds or the Labour-Greens cooperation agreement that has already been signed.
But they determine the number of each parties' MPs in Parliament.
The provisional results three weeks ago were: Labour on 49.1% (64 seats), National on 26.8% (35 seats), Act on 8% (10 seats), the Greens on 7.6% (10 seats), and the Māori Party with the seat of Waiariki.
The final results have Labour on 50% (65 seats), National on 25.6% (33 seats), Act on 7.6% (10 seats), the Greens on 7.9% (10 seats), and the Māori Party with 1.2% (two seats).