The cinema chain made the decision to make sure the safety of their staff and customers.
More than 100,000 people have signed a petition to remove The Lady of Heaven from UK cinemas.
The film was denounced by the Council of Mosques.
Baroness Fox said the decision was bad for the arts and bad for free speech.
The film was "underpinned with a sectarian ideology" and "misrepresents orthodox historical narratives and disrespects the most esteemed individuals of Islamic" according to an email from the chairman of the council of mosques.
The Muslim news site 5Pillars shared a picture of a group of Muslims protesting against the film at a cinema.
The executive producer of the film said that cinemas should defend their right to show films that people want to see.
He told the Guardian that he thinks cinemas are crumbling to the pressure.
Mr Javid said he was worried about the growing cancel culture in this country. There are people who think they have a right not to be offended, but no one else has that right.
Someone has a right to say what they want.
He warned that going down that road would be an incredibly dangerous one.
He said that the country has freedom of speech and expression.
Baroness Fox criticized calls to cancel the film, saying they were being used far beyond campus activism.
It's a lesson to those who argue identity politics aren't a threat to democracy.
The film tells the story of Lady Fatima, the daughter of the prophet Muhammad.
The depiction of the prophet Muhammad is seen as an insult in Islam.
The film's website says that performances are achieved through a unique synthesis of actors, in-camera effects, lighting and visual effects.
The film was described by the Muslim Council of Britain as divisive.
The organisation supports scholars and leaders who advocate for greater unity and for the common good.
Many of the film's supporters or those engaging in sectarianism in their response want to fuel hatred.
The film will be shown at a number of cinemas in London and south-eastern England.
Vue takes seriously the responsibilities that come with providing a platform for a wide variety of content and believes in showcasing films of interest to diverse communities.
The British Board of Film Classification will assess and rate a film before it can be shown. The Lady of Heaven can be seen in many of our cinemas.
The company wouldn't confirm if any screenings had been canceled, but said that decisions about how long a film remains on show are taken on a site-by-site basis.
Cineworld decided to cancel screenings of The Lady of Heaven nationwide due to recent incidents related to screenings of the film.