So far 11 flights have been cancelled due to strong winds.
A Wellington Airport spokesperson warned there may be further disruptions.
“Passengers are advised to check with their airlines for the latest information,” said the spokesperson.
Earlier, Flight NZ417 was forced to turn back to Auckland after strong winds prevented it from landing.
A strong wind watch, expected to last until 4pm, is in place for Wairarapa, Wellington and the Marlborough Sounds.
MetService warned the winds could become “severe gales” and cause damage to trees, powerlines and unsecured structures.
MetService meteorologist Mmathapelo Makgabutlane said Wellington Airport has recorded wind speeds of 98 km/h today.
MetService has issued a heavy rain watch for Tararua Range, the ranges of Westland south of Arthur’s Pass and the headwaters of the Canterbury lakes beginning at 1pm.
Makgabutlane said the heavy rain watch came with a risk of thunderstorms, including strong winds and possible hail. She said further watches are likely in the coming days.
“Because we’ve got this fast-moving weather system over the country, and winds are quite strong… those thunderstorms may be accompanied by quite gusty winds.”
By Thursday evening, thunderstorms are expected along the coastline all the way to Auckland.
MetService is reporting that this afternoon, there is a “moderate risk” of thunderstorms for Northland, western Auckland, western Waikato, Waitomo, Taumarunui, Taranaki, Tongariro National Park, Whanganui, Manawatū, Horowhenua and Kāpiti.
Makgabutlane said West Auckland is also in the firing line for thunderstorms this afternoon.
She said Auckland weather will worsen this afternoon.
Rain would “settle in” before rush hour and worsen during the night with thunderstorms possible.
“The winds are already starting to pick up... it is looking like they might get worse.”
Makgabutlane said the wild weather was connected to the Australian air mass flowing over the Tasman Sea.
The air mass also brought unseasonably warm temperatures to many areas of the country.
NIWA reported the top temperatures would “easily be in the low 20s” with some areas possibly getting to 25C.
A road snowfall warning is also in place for Milford Rd tonight starting at 9pm.