Featuring Deepika Padukone in the title role, Bhansali's period drama is facing the wrath of various Rajput groups and political leaders, who have accused the director of "distorting historical facts".
Addressing a Masterclass at the ongoing International Film Festival of India (IFFI), Shekhar said, "The intention of the filmmaker (Bhansali) was not to create controversy. He is a great filmmaker. But he has never been a political filmmaker. He wanted to make a great film, a big film.
The director, who received global acclaim for his films such as "Bandit Queen", and movies on the British monarch Queen Elizabeth I - "Elizabeth" and "Elizabeth: The Golden Age", recalled his run-ins with controversy.
Shekhar said when he was making the first Elizabeth (featuring Cate Blanchett) movie, there were constant statements in the media, criticising him for his portrayal of the queen.
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The director said such historical films are merely a "representation" or a "metaphor" of history.
He added, for him, the story of an individual is important if it tells a larger truth of the society today and that is why he chose to tell the story of infamous dacoit Phoolan Devi in "Bandit Queen".
Shekhar also revealed he had "changed" the speech Queen Elizabeth was supposed to have delivered to inspire 5,000 of her troops at Tilbury in wake of an expected invasion by the Spanish Armada.
"So she went back to her tent and said, 'This is what I said so write that draft now'."
He said knowledge of history in India is imparted in the form of a "moral tale", not a factual one.
"History is a constant interpretation of facts, I'm not saying it's wrong... This is how history works. In India, till the British came, we believed in mythology, not in history...