An AFP journalist witnessed clashes erupt between French police and civilians in St Louis, a heartland of the independence movement just south of the capital Noumea.
Public prosecutor Yves Dupas said security forces on an observation mission fired two shots after being “directly threatened by a group of armed individuals”.
The first “hit a man, aged 30, positioned as a lone gunman, in the right side of the abdomen”, Dupas said in a statement.
“The second shot hit a man, aged 29, in the chest.”
Police were looking for around a dozen people suspected of involvement in attacks on security forces.
“We’re not terrorists, we’re not in a state of war,” said one mother in the village where the security operation was taking place.
Unrest broke out in mid-May in New Caledonia over Paris’s plan for voting reforms that indigenous Kanak people fear would leave them in a permanent minority, crushing their hopes for independence.
Some demonstrators barricaded roads and burned or looted cars, businesses and public buildings.
France sent thousands of troops and police to the archipelago, almost 17,000km from Paris.
In violence not seen since the near-civil war of the 1980s, hundreds of people were injured and the material damage was estimated at around €2.2 billion.
The electoral change – which requires altering the French constitution – has effectively been in limbo since president Emmanuel Macron dissolved parliament for new elections that in July produced a lower house with no clear majority.
While unrest in the South Pacific territory has ebbed since mid-July, the road to St Louis in the south of the archipelago’s main island Grande Terre remains closed.
For the 1,200 inhabitants of St Louis, the only way in or out is by foot after presenting an ID at checkpoints in the north and south.
Only emergency services and ambulances can otherwise cross into the village.
Almost all other roadblocks across New Caledonia have been lifted, but a curfew between 10pm and 5am remains in place.
Since June 19, 13 pro-independence activists have been arrested.
Seven are currently in prison, including five in mainland France.