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First Union has made a formal complaint to the Labour Inspectorate at the Ministry of Business, Innovation and Employment.
First Union regional secretary Paul Watson said he had received a complaint from a member of the local community who was upset that the two supermarkets were openly advertising they would be open for business on Good Friday.
"This flagrant abuse of the Holidays Act is appalling," Mr Watson said.
"These supermarkets are already allowed to trade on Saturday, Sunday and Monday in Wanaka over the Easter weekend, allowing plenty of time for the local community and visitors to shop."
The point of the Holidays Act was to allow workers time off to rest with their families and for some, to acknowledge and observe the religious relevance of the Easter period.
The New World owners were completely out of line and were putting profits above the wellbeing of their workers, he said.
Foodstuffs head of corporate affairs Antoinette Laird said the holiday had come on the back of "a very challenging year" for the Queenstown and Wanaka community, who had been severely impacted by Covid-19 and the lack of international tourism to the area.
Many businesses were struggling and the Easter holiday was a time when local tourism could provide much-needed revenue for the local businesses, she said.
"In situations like this our store owners make an informed decision to put their community, staff and customers’ needs first and we know the local community appreciates the ability to be able to access much-needed groceries over the holidays.
"In order to meet the needs of the community, our Wanaka stores have taken the decision to open over the Easter holiday, just as many Queenstown businesses do."
Due to the small size of the town there was already a limited number of grocery options available to the local community and if the stores did not open, the sudden influx of Kiwi holidaymakers would really struggle to be able to satisfy their grocery needs.
MBIE regional manager labour inspectorate David Milne said it had "reached out" to major retail brands like Foodstuffs and Countdown to remind them of their obligations around restricted shop trading days.
The Labour Inspectorate did not disclose operational details relating to the enforcement of shop trading, he said.
Information on shop trading hours enforcement activity by the Labour Inspectorate over the Easter weekend would not be immediately available. It would be collated in the next four weeks, he said.
In 2017 retailers in Wanaka were given the green light to open legally on Easter Sunday for the first time after the Queenstown Lakes District Council voted earlier that year to relax the rules which had prohibited most retailers from opening.
In 2016, the Government changed the law, giving local councils the power to pass bylaws legalising trading on Easter Sunday.
Although trading remains restricted for most businesses on Good Friday, many shops in Wanaka have defied the law for years and opened for business as usual.
Dairies and service stations (with restrictions on what food and goods they can sell) cafes, restaurants, and souvenir shops are among those that can open on Good Friday.
Businesses that trade on Good Friday can be fined up to $1000, especially if they had been previously warned and prosecuted.