Four extra flights between Wellington and Auckland were being put on tomorrow to deal with any backlog.
• NZ6141 Auckland - Wellington 9.25am–10.30am
• NZ6142 Wellington – Auckland 11.05am–12.10pm
• NZ6143 Auckland – Wellington 1.15pm–2.20pm
• NZ6144 Wellington – Auckland 2.55pm–4.00pm
Meanwhile, KiwiRail's TranzAlpine service has been cancelled for Tuesday and Wednesday. The cancellation will affect 1416 passengers.
"We regret the inconvenience to our customersbut safety is paramount," said KiwiRail group general manager of sales and commercial Alan Piper.
"We're in close contact with our passengers, who are being offered a refund or the option to book alternative travel dates."
A rail charter service between Christchurch and Arthurs Pass had also been cancelled.
At this stage no Interislander sailings have been cancelled as a result of the weather, but general manager Mark Thompson said said they were carefully monitoring the weather and cancellations were possible.
"This is a developing situation and we are keeping a very close eye on the weather. Customers are being contacted and where possible being offered the opportunity to move to another sailing free of charge.
"We are sorry for any inconvenience to our passengers but safety is always our top priority."
Cyclone Gita has also closed State Highway 1 north and south of Kaikoura because of heavy rain and the risk of slips and rockfalls.
The New Zealand Transport Agency closed SH1 on both sides of the town, from Mangamaunu to Clarence and Peketa to Goose Bay, just after 8.30am. There have been some minor rockfalls on the Hundalees south of Oaro and also along the coast.
Route 70, the inland road via Waiau, remains open to Kaikoura.
Crews will aim to keep it open as long as possible. Drivers are urged to delay all but essential trips in the area until the severe weather has passed.
All drivers travelling from Picton to Christchurch are advised to take the Lewis Pass through Waipara and St Arnaud.
All highways are remain open on the West Coast and Nelson area. As steady rain falls, crews are working to keep stormwater drains open and roads free from flooding.
SH6 Whataroa to Haast is experiencing strong winds, especially around the river valleys. Extra care is required by drivers with caravans, campervans, high-sided vehicles and motorbikes.
SH6 Rocks Rd in Nelson is being monitored closely. Conditions will be assessed throughout the day and the road will be closed if conditions deteriorate.
NZTA senior journey manager Neil Walker said driving conditions will be difficult in affected areas, and roads may be closed at short notice for safety reasons. Slips, rockfalls, flooding and coastal inundation are possible.
Drivers are urged to keep a close eye on the latest road conditions and MetService forecasts before travelling.
"We're working closely with MetService, local authorities and the Civil Defence network in preparation for any impacts on the transport network and we're planning for the likelihood of road closures," Walker said.
"Vehicles need three times more stopping distance in the wet, while high-sided vehicles and motorbikes are more susceptible to tipping over in high winds."
If delaying travel is not an option, it's important that motorists to drive to the conditions during severe weather and reduce driving speeds, increase following distances and be alert to the possibility of surface flooding, fallen trees and debris.
All road closures and warnings will be updated in real time during the storm here, and drivers can also call 0800 44 44 49 for 24/7 updates on road conditions, closures or delays.
The latest severe weather information is available with MetService. For emergency and disaster updates visit Civil Defence.