"I unconditionally apologise. I never meant to hurt anyones feelings or sentiment," Kunder posted on his Twitter page.
The FIR against the director was registered yesterday in Lucknow based on a complaint filed by Amit Kumar Tiwari, Secretary of Thakurdwara Trust of Ayodhya.
In a series of tweets, which have now been deleted, Kunder had written, "Hoping a goon will stop rioting once he's allowed to rule is like expecting a rapist to stop raping once he's allowed to rape (sic)".
In another tweet, he had said: "Going by the logic of making a goon as CM so that he behaves, Dawood can be CBI director. And Mallya - RBI Governor (sic)."