Magnolia Bakery, which is credited for sparking a cupcake craze across the United States, had to close because it does not have a sink in the area where staff top cupcakes with pastel-coloured butter cream icing by hand.
The bakery said the inspection was deemed a "pre-opening inspection" because the business had new owners, having been bought in January by restaurateur and construction company owner Steven Abrams.
"Because the bakery has operated without this sink for the past 10 years we were unfortunately unaware we were required to install this equipment," the bakery said in a statement.
The bakery said it was also cited for a missing door handle, a missing light cover, and several mouse droppings and fruit flies by its garbage area.
"These last two violations come in spite of a thorough three times weekly rigorous extermination and internal inspection process," said the bakery which hoped to address each of the problems by Wednesday night.
Lines of people regularly wait in line for one of Magnolia's famed cupcakes, snaking around the corner and down the street from the bakery in New York City's West Village.