The song by Lucky Ali accompanied a sequence in the film which showed a Moharram procession.
"We did not intend to hurt anybody's religious sentiments through this song. I apologise, if in any way it has unintentionally done so. When the issue was brought to our notice we immediately addressed it," Nambiar said in a statement to PTI.
Recently representatives of the Muslim community raised objections to the portion of the film where the song has been used, after watching it.
"They came and saw the clip, after which we had a very long discussion pursuant to which the necessary and desired changes were made. The Central Board of Film Certification too has seen the film with the incorporated cuts and passed it with a U/A certificate. We hope our creative endeavour would be appreciated in the right spirit," Nambiar said.
The film, starring south actor Vikram, Neil Nitin Mukesh, Monica Dogra and Tabu, releases on February 1.
Recently the release of Kamal Haasan's 'Vishwaroopam' has been stalled after the Tamil Nadu government imposed a ban on its screening over allegations that the controversial film has anti-Muslim content.