This year's supreme winner, to be announced on April 23, had been judged four times.
Botswana Butchery, in the refurbished Auckland Ferry Building, was having some "teething problems around service", Wilson said.
"They have a universally highly praised restaurant in Queenstown. We would be surprised if Botswana Butchery in Auckland fell apart."
Restaurateur and MasterChef judge Simon Gault, who took out a full-page newspaper with a recipe for "Metro Food Critics' Testicles" in 2008 after a disagreement with the magazine, said it was a "little surprising" such a new restaurant made it to the top 50.
"Good luck to them. I hope they do well. Welcome to Auckland. It's always good to have a bit of competition, but I hope everybody realises that my steakhouse is the best in Auckland," he said, laughing.
NZ Herald reviewer John Gardner gave the food an eight out of 10 but the service a six. He wrote a waitress couldn't tell him about a dish without first returning to the kitchen to ask about it.
Herald on Sunday food critic Peter Calder gave it 3 stars and noted two dishes destined for his table went to a neighbouring one. "It all seemed a bit Fawltyesque for a branch of an established operation," he wrote.
This week Calder also said he found the restaurant's email-only booking system "colossally rude and unprofessional". Another critic, David MacGregor wrote on the Unscrewed website: "When quizzed the waitress wasn't able to answer a single question about the dishes."
Russell Gray, chief executive of the Good Group, which owned Botswana Butchery, said he was pleased to be on a list, despite being open only a short time. "We are not new to the industry, we have been successful in the hospitality game for a long time."
He said the eatery made the list by passing an "acid test" of a Metro judge's visit.
However, he agreed that they were working on improving standards of service.
"We are not trying to be a fine dining establishment, we are a fun dining establishment."