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Customers will need to present a vaccine pass to eat in its stores, which follows the framework under the government's new Covid-19 traffic light system.
However, those who are not vaccinated won't miss out entirely, with McDonald's confirming they will still be able to use the drive-through and delivery methods.
McDonald's spokesman Simon Kenny said: "Customers who go into restaurants will need My Vaccine Pass. We will continue to offer contactless service via drive-through and McDelivery, where My Vaccine Pass will not be required."
The moves as the country is set to move into the new traffic light system on Friday.
McDonald's won't be the first and only place the unvaccinated cannot enter.
Hospitality venues and close-contact businesses like gyms and bars will be able to stop unvaccinated customers from entering.
If you are not vaccinated, the traffic light system will likely feel like a level 3 lockdown.
Events, restaurants, hairdressers and cafes that use vaccine certificates will not be able to accept you into their stores.
Events, restaurants, hairdressers and cafes that do not use vaccine certificates will not be allowed to open at all under the red and orange settings - except to offer takeaway food only in the case of restaurants and cafes.
Gatherings at funerals and weddings will be limited to 10 people under the red setting and 50 people under orange.
Under the green setting, events, gyms and restaurants will be able to open without vaccine certificates but there will be restrictions on how many people can be in attendance.
Prime Minister Jacinda Ardern has said the vaccine passport is people's "golden ticket" to freedom.
"We know there are some still making the decision over when to be vaccinated – but we need to make decisions now that will protect them and others."