Netflix said the Tamil-language film - Annapoorani: The Goddess of Food - was removed at its "licensor's request".
The movie stars actor Nayanthara as a Hindu Brahmin woman who aspires to become a chef.
She is shown going against her family's religious beliefs and eating meat and learning to cook it.
Many Brahmins do not eat meat in accordance with rigid caste rules.
Members of hard-line Hindu organisations had objected to this and other scenes in the movie, including one where the actress is shown offering namaz, or Muslim prayers, before cooking biriyani.
Some Hindus also took offence at a scene where a Muslim character says that Hindu god Ram ate meat.
The film's producers have not officially commented on the issue yet.
A police case has also been filed in Madhya Pradesh state against Nayanthara and two others associated with the film.
Supporters of hard-line Hindu groups have accused many films and shows in recent years of insulting religious sentiments. In 2021, the cast and crew of an Amazon Prime show, Tandav, apologised after being accused of mocking Hindu gods.
Annapoorani released in theatres on 1 December and got mixed reviews from critics - it was praised for showing a woman from an orthodox family following her dreams, but some called it "an-all-you-can-eat buffet of undercooked subplots".
It was cleared by India's Central Board of Film Certification - known as the censor board - which reviews movies for public exhibition.
But the controversy began weeks later when people watched it on Netflix, where it began streaming on 29 December.
Last week, a man named Ramesh Solanki filed a police complaint in Mumbai objecting to several scenes - a case hasn't been registered there yet. Mr Solanki describes himself as a "proud Hindu Indian nationalist" on X (formerly Twitter).
Reuters reported that members of the hard-line Vishwa Hindu Parishad (VHP) shouted slogans outside the Netflix office in Mumbai.
On Thursday, Mr Solanki and a VHP spokesperson shared a letter of apology from Zee Entertainment Enterprises - the parent company of Zee Studios, which co-produced Annapoorani.
"We have no intentions as co-producers of the film to hurt the religious sentiments of the Hindus and Brahmins community," the letter said.
It also said the producers would address the concerns about the film and were working with Netflix to remove the film from its platform "until edited".
Zee did not respond to the BBC's email seeking comment.
While some said they were happy at the movie being taken off Netflix, others have expressed dismay. Actress Parvathy Thiruvothu said this would set a "dangerous precedent".
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