Air New Zealand spokeswoman Brigitte Ransom said the fog caused disruption to the airline's regional Link services.
MetService duty forecaster Liz Walsh said the fog was patchy and was looking like it would remain until around 9am, when southwesterly winds would dissipate the fog.
Fog is also causing problems at Hamilton Airport, grounding flights to both main centres and regional airports.
Three flights from Hamilton to Wellington have been cancelled and a further 12 flights from Hamilton to Auckland, Palmerston North, Christchurch and Wellington Airports have been delayed by more than 45 minutes.