Commuters walk past a Chick-fil-A freestanding franchise in New York, Oct. 3, 2015. Reuters / Rashid Umar Abbasi

Hungry Manhattanites, your chicken sandwich from a certain fast-food chain will have to wait. New York City's first standalone Chick-fil-A restaurant, located in midtown, will remain closed, the company announced on Monday following its initial closure last Wednesday for health violations.

The company announced in a statement that the Manhattan location would remain shuttered for the time being. "We do have a little more work to complete so we have made the decision to remain closed until we feel confident we are exceeding standards in all areas," the statement read.

The location closed on Dec. 30 after an inspection on Christmas Eve ended in 59 violation points for infractions that included food not being protected from potential contamination, the presence of flies and cold food stored at too-warm temperatures. More than 28 violation points would result in a "C" score, the worst grade a restaurant can receive in the New York City system, although the Chick-fil-A at 37th Street and Sixth Avenue was listed as "grade pending," WABC in New York reported.

"There were six violations on the last health inspection, so we decided to voluntarily close the restaurant so that the team could focus solely on those issues—primarily the presence of fruit flies," spokeswoman Amanda Hannah told CNBC. In its statement on Monday, Chick-fil-A said it was working toward fixing the issues at its midtown restaurant.

"Closing the restaurant voluntarily has allowed us the time to make facility and procedural changes that will better meet the needs of serving our guests while operating in a very busy urban environment," the statement read. "These changes have included retraining the leadership team and employees, fruit fly mitigation and thorough cleanings of the restaurant, independent inspections by an outside consultant and equipment and facilities upgrades."

Chick-fil-A, known for its chicken sandwiches and waffle fries, opened its first standalone New York City location in October, but New York University has had a location in its food court for more than a decade.