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Flight NZ8857 on Thursday last week eventually departed 30 minutes late with the unmasked pair onboard, after staff confirmed they had an exemption.
Air New Zealand would not confirm how the two people proved they were exempt from having to wear a mask, but the Herald understands they did not have an official Covid exemption card.
A passenger onboard the flight tweeted about the incident, saying 'an anti-masker without documentation held everyone up for half an hour'.
They said staff eventually gave up and took off with the passenger onboard.
Nelson had 20 active cases of Covid-19 as of Wednesday, with one case from the current outbreak having recovered. One person is in hospital in the region.
Investigations into the source of infections are ongoing, and public health officials are continuing to manage several hundred contacts associated with exposures at two schools - Broadgreen Intermediate and Enner Glynn school.
Air New Zealand's current Covid-19 policy states that face masks or coverings are required on all flights in all traffic light levels.
However official Government guidelines said passengers don't need to show proof of an exemption to not wear a mask on a flight, but it is highly recommended.
E Tū Union Head of Aviation Savage said those rules should change to require proof of mask exemptions to be shown before boarding a flight.
This would help stop unruly passengers getting on planes he said.
"We just want to make sure that if someone has got an exemption for wearing a mask that the cabin crew or the ground staff are not having to confront that person or get themselves into any situation where a person is going to get offended for being asked."
Savage said they were seeing more people not wanting to wear a mask as the discussion around vaccines became more polarised.
"Particularly because of the controversy for some people around vaccinations, there are more people who are making a show of the fact they don't want to wear a mask."
He also said there are issues with people extending the time they're not wearing a mask after eating and drinking.
Savage said mask-wearing was really important for protecting not only passengers but cabin crew, particularly as Covid becomes more commonplace.
Epidemiologist Professor Michael Baker agreed there should be a requirement to demonstrate mask exemptions on flights.
"It's a bit like someone getting on a plane and saying I don't have my vaccination record on my phone or any evidence I have been vaccinated, you just have to take my word for it."
The policy for travelling onboard an Air New Zealand domestic flight will change again next week when the Auckland border opens on December 15.
People will either have to show their vaccine pass or present a negative Covid-19 test within 72 hours of travelling.
Baker said masks are an important factor of protecting people from Covid-19, particularly in enclosed spaces like aircraft.
"I think most of us would feel concerned if someone sitting next to us on a flight wasn't wearing a mask without a valid reason."
He told the Herald it was important we had well understood, valid, simple methods for documenting why people are exempt from mask requirements.
When asked about the incident, Covid-19 Response Minister Chris Hipkins' office said there had been no change to the guidance around mask wearing on flights and referred further questions to Air New Zealand.
Air New Zealand said since the mask mandate came into effect on November 18 2020, 11 customers had been denied travel for failing to comply.
The airline said overwhelmingly, customers have been supportive of the Government requirement to wear a face covering on board flights.
- By Nick James