Turnout was only 41.60 percent as pro-independence campaigners boycotted the vote, saying "a fair campaign" is not possible with high Covid-19 infection numbers.
Residents of the Pacific territory of New Caledonia have voted overwhelmingly to remain part of France in a third referendum that was boycotted by pro-independence groups.
With all ballots counted from the referendum on Sunday, 96.49 percent were against independence, while only 3.51 percent were in favour, with turn-out a mere 43.90 percent, results from the islands' high commission showed.
Police reinforcements have been sent to the territory known as "the pebble", which is of strategic importance to France and is part of a wider tussle for influence in the Pacific between Western countries and China.
The archipelago of about 185,000 voters, 2,000 kilometres (1,250 miles) east of Australia, was granted three independence referendums under a 1988 deal aimed at easing tensions on the islands.
Having rejected a breakaway from France in 2018 and then again last year, in this last referendum the inhabitants were asked one last time: "Do you want New Caledonia to accede to full sovereignty and become independent?"
Boycott over Covid
The indigenous Kanak population, who largely favour independence, have called for non-participation in the referendum as they are in a 12-month mourning period following September's surge in Delta infections of the coronavirus.
"I don't want to go and vote because I don't agree with this final poll," said Jean-Pierre Wadra, a resident of the capital Noumea.
New Caledonia's 270,000 inhabitants were largely spared during the pandemic's first phase, but have suffered close to 300 Covid-19 deaths since the recent appearance of the Delta variant.
The pro-independence movement has still threatened non-recognition of the referendum outcome and vowed to appeal to the United Nations to have it canceled.
The pro-French camp, meanwhile, had called on supporters to turn out, fearing the boycott by pro-independence parties may prompt them to stay at home with victory looking like a foregone conclusion.
"It is important that the mobilisation of the no-independence supporters remains absolute, to show that they are in a majority and united in their wish for New Caledonia to remain part of the French republic," said Thierry Santa, president of the conservative Rassemblement-LR party.
In June, various political parties agreed with the French government that the referendum, whatever its outcome, should lead to "a period of stability and convergence" and be followed by a new referendum by June 2023 which would decide on the "project" New Caledonia's people want to pursue.
But hopes for a smooth transition were jolted when the main indigenous pro-independence movement, the FLNKS, deemed the government's insistence on going ahead with the referendum "a declaration of war".
The pro-Paris side won the 2018 referendum with 56.7 percent of the vote, but that fell to 53.3 percent in the 2020 election.
The vote comes against the backdrop of increasingly strained ties between Paris and its regional allies.
France regards itself as a major Indo-Pacific player thanks to overseas territories such as New Caledonia.
President Emmanuel Macron has insisted the French state takes no side in the referendum, other than to ensure fair and smooth proceedings.