"Under this interpretation of the Act and the regulations, we would conclude that Brockville Four Square cannot be considered a grocery store for the purposes of licensing," Mole said.
The shop did not appear to meet the requirements for a different off-licence application, documents showed.
Mole said it was the first such case in Dunedin.
Foodstuffs New Zealand government relations general manager Melissa Hodd said tobacco sales revenue had risen "steeply, very quickly and disproportionately to food" as a result of the government policy of increasing excise tax on tobacco products.
The impact the revenue increase was having on licensing decisions was an unintended consequence of tobacco tax. Foodstuffs was in talks with the Government about the issue. It was the first case Foodstuffs had faced in Otago, but it was an increasing problem throughout New Zealand, she said.
"While the business has had this issue on the radar since the implementation of the Sale and Supply of Liquor Act 2012, it has only become a problem recently as the tobacco tax hikes are coming into effect."
In 2016 the Medical Officer of Health overturned a decision by the Whangarei district licensing committee to renew an off-licence for a grocery shop. Tobacco accounted for 50 per cent of sales revenue, and the committee did not give proper weight to the fact food was not the shop's principal business, it was found.
The shop was not granted a licence renewal.
Cockle Bay Four Square, in Auckland, also had its liquor licence renewal application declined last year on the basis it sold too much tobacco to be considered a grocery shop. The owners of Brockville Four Square declined to comment.
The Alcohol Regulatory and Licensing Authority did not respond to questions.