The ballot comes six months after a closer-than-expected referendum raised questions over France's grip on the strategic islands, which sit on a quarter of the world's known supplies of nickel, a vital electronics componen.
The November 6 referendum result showed 56.7 percent voted to stay French, a much tighter outcome than predicted.
Turnout on Sunday was 58.49 percent at one hour before the polls closed at 6pm (0700 GMT), about 15 percent less less than in the referendum at the same time, the high commission said.
Under a 1998 agreement, there can be two further votes on independence before 2022 in the archipelago located more than 1,000 kilometres (600 miles) northeast of Brisbane, Australia.
In the outgoing local Congress, pro-independence factions held 25 of the 54 seats but are hoping to win a majority when results are released later Sunday evening.
Supporters of independence for the islands, fringed by stunning beaches, are mostly ethnic Kanaks who make up less than half the population of 269,000 people.
1998 peace deal
White residents -- descendants of early European settlers as well as more recent arrivals -- overwhelmingly want to stay French. They are joined by other Pacific minorities.
Last November's referendum was the culmination of the 1998 peace deal which followed a quasi-civil war between Kanaks and whites that left more than 70 dead in the 1980s.
The "Noumea deal" has also paved the way for the islands to become increasingly autonomous, with wide areas of policy under the control of local authorities.
Almost 170,000 people were eligible to cast ballots on Sunday, with more than 900 candidates running.
There are 76 elected provincial representatives, 54 of whom will sit in the Congress.
Voting is restricted to the "population concerned" with the archipelago's political future and requires electors to have been resident at least since 1998.