A French-operated flight will bring stranded New Zealanders to Brisbane, with a New Zealand Defence Force flight arranged for the travel from Brisbane to New Zealand.
The French flight is due to depart Tontouta Airport at 6pm NZ time with 49 Kiwis on board.
The flight from Brisbane to Auckland is due to arrive at Auckland International Airport at 1am NZ time.
MFAT said it was still working with French and Australian authorities on logistics.
Around 10pm last night a Defence Force flight completed the first mercy mission, landing in Auckland with 48 New Zealanders on board.
MFAT said 260 New Zealanders remain and are hoping to leave Noumea (of the 274 NZers in New Caledonia registered on Safetravel).
It is believed that in total there would have been at least 371 NZers in New Caledonia when the conflict erupted.
It has claimed six lives while millions of dollars in damages has been caused to businesses and infrastructure.
French President Emmanuel Macon is due to arrive in New Caledonia this evening.