Foreign Affairs Minister Winston Peters has confirmed it is the first in a series of proposed flights.
In an online post about 2.20pm Peters said the flight had departed, from Whenuapai Air Base in Auckland.
Peters said the flight would carry about 50 passengers with the most pressing needs from Nouméa back to Auckland.
Passengers for subsequent flights would be prioritised by consular staff.
"New Zealanders in New Caledonia have faced a challenging few days - and bringing them home has been an urgent priority for the government," Peters said.
"We want to acknowledge the support of relevant authorities, both in Paris and Nouméa, in facilitating this flight."
Peters said the situation in New Caledonia was "dynamic" and New Zealand officials were working with French counterparts and other partners, like Australia, to learn what was needed to ensure safety of their people there.
"In cooperation with France and Australia, we are working on subsequent flights in coming days."
Peters said New Zealanders in New Caledonia were urged to make sure their details on SafeTravel were up to date.
This would allow officials to be in touch with further advice.
Meanwhile, a New Zealander desperate to return home said it was heartening to know that a flight was on its way.
Barbara Graham, who was due to fly home from a research trip in New Caledonia on Monday, had been on holiday there with her husband and six-year-old son last month.
She said she was desperate to get home to them, but knew others were in greater need.
"It's really really heartening to hear that the flights have started and I'm extremely pleased they're prioritising the people that really really need to get home, you know parents and children, I can't imagine what it would've been like if my son had still been here in this situation."
A nearby bakery was selling rationed bread to residents and visitors, Graham said.
