The movie, which was released across the world Friday, is based on the Sri Lankan civil war and also shows the 1991 assassination of former Indian prime minister Rajiv Gandhi.
Actor John Abraham, who has co-produced the film, also features as an Indian Army intelligence agent sent to Sri Lanka.
The film sparked protests across the world even before it got released as Tamil groups claimed that the film portrays the Liberation Tigers of Tamil Eelam in poor light.
In Canada, the movie was released in six theatres in Surrey, Montreal and Toronto.
Though the company representing the film claimed that it was being pulled from theatres in Canada due to protests, spokeswoman for Cineplex Entertainment, Pat Marshall, said that it was being pulled from only two Toronto theatres screening the Tamil version, the Vancouver Desi reported.
"It's the way that our business works, it's our guests who decide what movies stay on the screen and what movies come off by buying the ticket, ` she was quoted as saying.
According to Marshall, the film was received well in four of the six theatres screening the Hindi version, while the two Toronto theatres screening the Tamil version could not work.
`The Hindi version opened well. The two locations in the GTA (Greater Toronto Area), in the Tamil version, did not open well, ` Marshall said.
`Of those six locations, given the performance, the two Tamil version movies will come off but the other four will continue on because they've done well, ` she added.
A group of around 50 people protested outside Toronto's Eglinton Town Centre theatre.
The movie, directed by Shoojit Sircar, also features Nargis Fakhri, Ajay Rathnam and Leena Maria Paul.
Though India's Central Board of Film Certification had passed the film, it has been pulled from some theatres in Britain and in Chennai in the south Indian state of Tamil Nadu.