The Caledonian Union accused the head of the territory’s administration, Philippe Gomes, of reneging on an agreement struck last July to fly the Kanak flag, a symbol of the indigenous population, alongside the French tricolour.
New Caledonia was a French territory until 1999. But the 1998 Noumea Accord resolved that powers of government would gradually be transferred from France over the following 15-20 years.
The agreement also states that the territory should hold a referendum on full independence from France between 2014 and 2019.
The congress is due to elect a new government on 3 March but Gomes said his party would resign in the hope of forcing Paris to call an election in the territory.
The 230,000-strong island group is divided between Kanaks, a Melanesian ethnic group who make up about 44 per cent of the population, and ethnic Europeans, who make up 34 per cent.