L2: Empuraan begins with the backstory of a character Zayed Masood - played by director Prithviraj - who was orphaned during riots in a place in India, with some of the details being similar to the religious violence that occurred in 2002 when Modi was chief minister of Gujarat state.
The long flashback sequence shows some graphic scenes depicting Hindus committing violent crimes against Muslims during the violence.
It also shows how one of the perpetrators of the violence becomes more powerful over the years and is seeking to secure a key position in Kerala's political landscape.
The scenes sparked an uproar.
Rajeev Chandrasekhar, the state president of the BJP, who had wished the film's team well before its release, later said that he now realised there were "topics in the movie that disturbed Mohanlal fans and other viewers".
"A movie should be watched as a movie. It can't be seen as history. Also, any movie that tries to build a story by distorting the truth is doomed to fail," he said, adding that he would not watch the film.
While some state BJP leaders supported this, others criticised the makers and accused them of depicting "anti-national themes" in the film.
The Organiser Weekly - a magazine published by the Rashtriya Swayamsevak Sangh (RSS), which is the ideological parent of the BJP - called the film a "disturbing, divisive tale disguised as cinema".
"Empuraan isn't just a bad film; it's an attack on faith, on political plurality and on the very soul of balanced storytelling," its review said.
Some social media users have also called for a boycott of the film, but there has not been a large-scale online campaign or big protests against the movie.