Just over 53 percent of the electorate opted for the status quo in the second of three possible referendums under the Noumea Accord.
180,000 voters, who are on a roll restricted to indigenous Kanaks and long-term residents, were allowed to decide whether the territory should assume full sovereignty.
The results showed a sharp divide between the two camps, with some communes voting with more than 90 percent either for or against independence.
Turnout was above 85 percent, exceeding the 81 percent in the first referendum in 2018 when just over 56 percent voted for the status quo.
There were reports of voter intimidation at several polling stations.
The pro-independence Caledonian Union issued a statement calling on the public to accept the verdict.
In a first reaction, a senior FLNKS member Roch Wamytan said he would want to go to a third referendum in the quest of the indigenous people to regain control of their country.
French President Emmanuel Macron said that as head of state, he saluted this show of confidence in the Republic with a profound feeling of gratitude.