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By Katie Little, CNBC

After years of waiting for Chick-fil-A to open a full-menu Manhattan outpost, Big Apple fans have gotten some unwanted news in the new year.

The eagerly awaited Herald Square location has been closed for days now. It first shuttered Wednesday after city health inspectors found several violations at the restaurant.

People walk past a new Chick-fil-A restaurant, Thursday, Oct. 1, 2015 in New York. The Atlanta-based privately held franchise company has more than 1,900 restaurants in 41 states and Washington, D.C.Mark Lennihan / AP

"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.

"There is a little more work to be done from a facilities, maintenance and retraining standpoint, so we have decided to remain closed (Monday) until we feel everything exceeds standards," she added.

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While Chick-fil-A's footprint is still relatively small in the Northeast, it has ambitious expansion plans outside of its traditional Southeastern stronghold. Currently, it is the eighth biggest chain by U.S. sales, according to market research firm Technomic's latest report.