New Caledonia's 54-seat Congress will have to hold a fresh election of a new government after the pro-independence FLNKS resigned from the administration chosen just hours earlier.
The FLNKS said there was an error in the balloting that cost it a seat in the 11-strong government which is chosen in proportion to the parties' relative strength in the congress.
Eight anti-independence ministers had been selected and three pro-independence ministers when the election went ahead on Monday.
Last week, the two dominant pro-French parties, the Rassemblement UMP and Future Together, struck a power sharing deal.
After the Rassemblement's success in the French assembly election in June, the government of Marie-Noelle Themereau resigned last month which prompted Congress to choose a new government.
The deal reached last week provides for the Future Together's Harold Martin to be elected as the new president.