Chopra had apologised on Twitter after many Indians expressed outrage at an episode of her television drama Quantico that showed a Hindu terrorist plotting an attack in Manhattan, with the intention of blaming it on Pakistan.
It was at the restaurant that Kochhar won his first Michelin star in 2001, also the first for an Indian chef in the history of the Michelin guide.
The hotel, which houses the Rang Mahal restaurant set up by Kochhar, said: "Following the recent comments made by Chef Atul Kochhar, we have taken the decision to end our agreement with him for Rang Mahal. With the termination of our agreement, Chef Atul will no longer be associated with the restaurant", Bill Keffer, general manager of the hotel, was quoted as saying by Gulf News.
Arab journalist Khalid Ameena later tweeted: "You (Kochhar) have offended me.As a person who loves India its people no matter what their caste or creed".
A section of Twitter users even called on JW Marriot to fire the chef and other said that they would boycott the restaurant. "Shame on You", he tweeted to his nearly 57,000 followers.
In another apology tweet made in wee hours of Wednesday, Kochhar wrote, "I would like to apologise unreservedly to my Muslim friends, the Islamic community and everyone I have offended with my recent tweets".
According to the hotel, the restaurant will continue to operate without the chef's affiliation.
He issued an apology on Twitter that read: "There is no justification for my tweet, a major error made in the heat of the moment on Sunday". The second apology was issued after several social media users pointed out that Kochhar had only acknowledged that Islam was founded 1,400 years ago but had not apologised for his purported bigotry. Many also criticised him for working in a Muslim country while spreading negative messages about Islam. "We would like to stress that we do not share the same views as stated in the remark, nor is it a representation of the culture of diversity and inclusion that we pride ourselves on at the hotel", the hotel tweeted on Monday.