Wellington Airport says at least 48 flights have been disrupted by low hanging cloud so far today.
Air New Zealand, Sounds Air and Golden Bay Air have cancelled several regional flights today.
Other flights have been delayed or diverted.
It is the third day in a row there has been disruption at Wellington airport. On Sunday, 35 flights were cancelled after a low fog rolled in.
Disruptions continued on Monday with the weather leaving a number of Air New Zealand aircraft out of place.
Several flights were cancelled and passengers rebooked or credited.
A spokesperson for Wellington Airport said: "Unfortunately the low cloud remains and is still causing major disruptions. There have been 48 cancellations so far and eight diversions. Larger jets have been unable to land for the last few hours so it is very quiet here now in terms of aircraft activity."
Air New Zealand confirmed today that it had again cancelled several flights into and out of Wellington due to low-lying cloud.
Air NZ chief operational integrity and safety officer Captain David Morgan said Airways was currently upgrading its instrument landing system "which is the system that provides guidance for our pilots on their approach to land. Due to the upgrade of this system, low cloud is disrupting flights on our Q300 and ATR aircraft more than usual".
MetService said visibility at the airport this morning was up to 13km, which was down to 2km this afternoon.
The forecaster said the low cloud was expected to improve mid-afternoon, but some could linger through the evening.