The shutdown came after the restaurant was found to have even more problems during a Christmas eve re-inspection due to a poor score on December 15, 2015. But a spokesman for the New York City Department of Health and Mental Hygiene, the agency that oversees the inspection program, said that the violations are serious enough to result in a grade of "C" without a successful appeal.

Just months after opening, New York City's first Chick-fil-A, closed its doors for five days after an inspection on December 24, in which the restaurant received 59 violation points.

"There were six violations on the last health inspection, so we made a decision to voluntarily close the restaurant so that the team could focus exclusively on those issues-primarily the presence of fruit flies", spokeswoman Amanda Hannah told CNBC. According to the NYC Health department, more than 28 violation points would get a restaurant a "C" grade - the worst grade a restaurant can get in the city.

Daily Mail Online has contacted Chick-fil-A for further comment. Filth flies include house flies, little house flies, blow flies, bottle flies and flesh flies. Harborage or conditions conducive to attracting vermin to the premises and/or allowing vermin to exist.

The restaurant was initially expected to reopen Monday, but in a statement Chick-fil-A officials said the restaurant would remain closed "until we feel confident we are exceeding standards in all areas".

It says it wants to "ensure the cleanest and safest environment going forward".

Chick-fil-A's Manhattan store opened to great fanfare in October, offering free food to its first customers as it launched an attempt to rival the likes of McDonald's in the city.