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A High Court judge ruled the supermarket company, which runs the chains New World and Pak'NSave, deliberately used covenants on land to hinder rivals.
This came to light in a Commerce Commission market study in 2022.
Justice Paul James Radich said the practice was to hinder rivals opening in three locations - Newtown and Petone in Wellington and Tamatea in south Napier.
Commission chairperson John Small said the penalty showed the seriousness of the conduct.
It decided to take the case to court because he said anti-competitive measures should not be tolerated.
Small said Foodstuffs North Island had stopped using the covenants - or restrictions on land - which were in place for 99 years.
The penalty was the largest imposed so far under section 28 of the Commerce Act and the commission had pursued the court action even though land covenants were illegal, he said.
"The covenants were of very long duration - up to 99 years - and lodged with the purpose of hindering competitors in local towns and suburbs where Kiwi consumers buy their groceries.
"By blocking other supermarkets from opening new stores or expanding existing ones, the covenants hindered competition for Kiwi shoppers.
"A penalty of this magnitude sends a clear message that this kind of anti-competitive conduct will not be tolerated."
Small said the case against Foodstuffs North Island should act as a deterrent to businesses and a reminder the commission would continue to pursue companies in any industry who used land covenants to stop rivals entering local markets.
"Land covenants can harm competition by raising barriers to entry or expansion in a market, making it harder for rival businesses to compete effectively and gain scale.
"They deprive Kiwi consumers of the benefits that come from a more competitive market."
Small said Foodstuffs North Island committed to stop using restrictive land covenants in 2021 and had started to identify and remove clauses in existing tenancy contracts.
Justice Radich said the penalty imposed recognised the fact the conduct was historic and the defendants had admitted the conduct at the earliest possible stage.
He also said Foodstuffs North Island had not intended to breach the law and the covenants were not enforced.