Countdown customers will have to use payWave and pack their own groceries during the nationwide restrictions, the supermarket says.
Perspex screens will also be erected at checkouts, limited numbers let inside stores at one time and every second checkout will be closed - self serve included.
The news comes after 40 new cases of Covid-19 in New Zealand were announced yesterday afternoon by Director-General of Health Dr Ashley Bloomfield.
The country also has 13 probable cases, taking the nationwide combined total of confirmed and probable cases to 155.
To combat the increasing spread of the virus, Prime Minister Jacinda Ardern announced on Monday that the country would be locked down for four weeks from midnight tonight.
Countdown and other supermarkets, deemed essential businesses, will remain open during the lockdown.
However, from today Countdown stores will introduce several additional measures to ensure the safety of staff and customers.
Countdown general manager of health and safety, Kiri Hannifin, said the supermarket understood that for some the changes would be upsetting.
However, the supermarket chain wanted to play its part in preventing the spread of the potentially deadly virus.
"We're determined to keep providing New Zealanders with access to our stores, while also making sure we're providing our team and customers a safe and healthy environment to shop in," Hannifin said.
"These new measures are in addition to the other changes many customers will have seen in place already, including new markings at the checkouts, which provide a physical distancing guide."
Limiting the number of customers in our store at any one time:
"The number allowed will depend on the size of the store and will be managed via security," Hannifin said.
"The number of people per store will be dependent on the size of a store. This action means customers can maintain physical distance between each other and our team."
Closing every second self-service checkout and every second checkout:
"This will again ensure we are providing enough space for customers to maintain a physical distance from each other and our team."
Customers will need to pack their own groceries, temporarily:
"This will help speed up the checkout process and ensure we can move customers through our stores quickly and efficiently, and keep any queues of people outside our stores moving. It will also limit the handling of items being bought."
Perspex screens at checkout rolling out in stores:
"These screens will help protect both team and customers from any sneezes or coughs, and will begin being rolled out in our stores from [Wednesday]."
We are asking customers to use payWave wherever possible:
"This will help cut down on the handling of bank cards."