Geranium, the first eatery in Denmark to receive top Michelin honours, had been storing fresh shellfish like oysters, crayfish and scallops at too-high temperatures over an extended period, the Danish Food Administration wrote after an inspection.
Two walk-in coolers also had "black, green and white splotches growing on the underside of shelves and on packaged pickled garlic," according to a report dated September 29th but only cited by Danish media on Thursday.
The regulator slapped the Copenhagen restaurant -- which charges 2,000 kroner for a meal without drinks -- with a frowning "smiley", the lowest grade of its four-tier system.
"I do not agree with what is written. I believe that it is greatly exaggerated but I admit that there are some parts of the process where perhaps we have been a bit unattentive," Geranium chef Rasmus Kofoed told Danish news agency Ritzau.
The restaurant had been using a computerised system to monitor food temperatures incorrectly, but fish and shellfish were always stored on ice regardless of the surrounding temperature, he added.
This year the Nordic edition of the Michelin Guide gave three stars to Geranium, but only two to Copenhagen's celebrated Noma, which was named best restaurant in the world by Britain's Restaurant magazine in 2010, 2011, 2012 and 2014.
Noma too faced criticism from the Danish food safety regulator in 2013, when it was accused of not taking adequate action after a sick kitchen worker gave dozens of customers a nasty case of food poisoning.