Tokelau, three atolls with a total area of 12 square kilometers of land (4.6 square miles) and a population of about 1518 people, could have become the second smallest independent nation after the Vatican.
Of the region's 789 people, eligible to vote, 692 took part in the ballot, with a total of 446 (or 64.4%) voting for self-government in free association with New Zealand, which was only 16 short of the required two-thirds majority.
UN Secretary-General Ban Ki-moon "has followed with interest the referendum", his press service said in a statement.
"He takes note of the results and respects the decision of the people of Tokelau not to move to self-government in free association with New Zealand," the statement says. "It is important that the people of Tokelau have had this opportunity."
In a similar ballot in February 2006, 60% voted in favor of independence, with the losing margin of 36 votes.
It is still unclear whether the third attempt to lift the status of the Non-Self-Governing-Territory will be held in one of the world's most remote territories.
Tokelau has no airport or shipping ports, and it takes a 28-hour boat trip to reach it from the nearest island of Samoa.
Some 16 Non-Self-Governing Territories still remain on the UN's decolonization list, compared to 72 in 1945.
