Chef’s Table at Brooklyn Fare, a highly acclaimed restaurant with three Michelin stars, has closed amid a legal dispute between its chef and owner, leaving a culinary void for customers of fine dining in New York City, where the restaurant had been a top-dollar fixture of flavorful creativity for more than a decade.

The restaurant, which served an extensive tasting menu inspired by Japanese seafood and French cooking techniques, closed in July after its chef, César Ramirez, was fired by the owner, Moneer Issa, according to court records.

In July, Mr. Ramirez filed a lawsuit in State Supreme Court in Brooklyn against Mr. Issa and the restaurant’s holding company, Manhattan Fare Corp, claiming that he had been “arbitrarily terminated” and was owed tens of millions of dollars for defamation, unpaid wages and other damages.

In an affidavit filed in August, Mr. Issa said that he had fired Mr. Ramirez because he had stolen company property that was worth more than $100,000, including dishware, oven parts and wine cases.

Mr. Issa also accused Mr. Ramirez of having “actively recruited restaurant staff to leave” the restaurant and join him on a new venture that he had been planning, which violated the stockholders’ agreement, the affidavit states.

Mr. Ramirez said in his complaint that “at his own personal cost,” he had purchased “very high end and expensive equipment” that would be suitable “for the most elegant, luxurious and discriminating gourmet tastes.” He added that the equipment had been lent without charge to Mr. Issa for the restaurant.

Mr. Ramirez and Mr. Issa did not immediately respond to calls seeking comment on Friday.

The closure, which was reported by Business Insider on Friday, stunned fans of the high-end restaurant, which first opened its doors in 2009 in Downtown Brooklyn before moving in 2016 to Hell’s Kitchen in Manhattan, where Mr. Ramirez and his staff would cook in a small space at the back of a supermarket for a handful of guests each night.

The restaurant had widely been considered among the best fine dining establishments in New York City. The New York Times named it the sixth-best restaurant in New York City this year.

A spokesman for Brooklyn Fare Management, which Mr. Issa owns, said in an email that the restaurant would reopen in October and that a new creative team would be announced at a later date.

“We will have an announcement around a new creative team with a track record that demonstrates they can meet and exceed our exacting standards for service and culinary sophistication,” the spokesman said.

It was unclear who the chef would be if the celebrated restaurant reopens.

Guests of Chef’s Table at Brooklyn Fare booked tables months in advance, and the tasting menu cost $430 per person.

In 2011, The New York Times reviewed the restaurant and gave it three stars.

The review described an intimate atmosphere inside the restaurant, with Mr. Ramirez and his staff appearing “intensely focused, sometimes robotic” until it was time to present each dish, at which point the mood among guests would swing from “hushed to giddy.”

The single-bite dishes included Japanese snapper with an olive-oil ponzu sauce and crispy leeks; fluke with pickled daikon; a single kumamoto oyster suspended over a gelée made of oyster liquor.