After undergoing a last health check, the evacuees left the Whangaparaoa military base and travelled by bus to the airport.
98 New Zealanders left by bus or with family and friends.
The base will soon be back in use as a quarantine centre. Eight New Zealanders on board the Diamond Princess cruise ship are due to leave Japan late on Wednesday night on an Australian evacuation flight to Darwin.
Of the 14 New Zealanders originally on board the ship, two are still in hospital in Japan and a family member has stayed with them.
Eight people will take flight to Darwin, and from there will be brought to Auckland on a flight arranged by New Zealand. When they arrive they will be taken to quarantine at the Whangaparaoa base.
Latest official figures from China say 1,868 have died from coronavirus.