Queenstown Airport's GM of Operations and Safety, Mike Clay, said the airport had been working with airports to increase capacity before the cut off, but they needed more time.
"There will be people in Queenstown and surrounds who are effectively stuck if repatriation flights are not able to operate after the cut-off this evening," he told the Herald this Morning.
A total of 22 departing flights are operating out of Queenstown today for New Zealanders to return home today, with additional seats. However Clay said it was clear there was still "more demand than capacity available today"
Many holidaymakers who found their trips cut short were redirected via Invercargill or Christchurch airport, due to the high demand for seats out of Queenstown.
After this grace period the domestic network will be greatly reduced. At Level 4 physical distancing and proof of 'essential travel' will also be required on planes.
After the bubble: What to do if you still need to fly
Following the grace period Air New Zealand says it will be operating a "very limited domestic schedule."
From Friday flights will be for "essential travel" only. Passengers travelling after the bubble will be required to carry a letter to prove their travel is essential - as outlined by the Government's Covid 19 guidelines.
If your travel is of an essential nature - you will have to call your airline's Contact Centre to rebook your tickets.
Other customers who are booked to travel from Friday will receive a cancellation email, and their bookings will be held in credit for 12 months, with another 12 months to travel.
From Friday, there will be just seven daily routes on the network.
These are links between Auckland, Wellington and Christchurch. There will be one daily service between Nelson and Wellington, and Christchurch to Dunedin.
After this 'grace period', physical distancing will be required by the Ministry of Transport on aircraft under alert Level 4, further reducing air capacity.
Qantas-owned carrier Jetstar said that its services would continue as scheduled until midnight, tonight.
"We are currently reviewing our schedule and some flights may be cancelled whilst some services may remain in place to allow essential travel to continue," the airline said in a statement.
Previous level 3 and 4 lockdowns have seen the carrier ground their New Zealand services.
For more information, passengers booked to travel with on Jetstar should visit their travel alerts page
Those flying with Air New Zealand should visit their COVID-19 Hub