A Pakistani minister suggested Delhi provide security after Khan wrote an account of how it felt to be a Muslim in India.
Khan said the article had been given an “unwarranted twist” and he could not understand the controversy.
Khan is one of Bollywood’s biggest stars with fans all over the world.
The actor wrote in Outlook Turning Points – published by India’s Outlook magazine in association with the New York Times – that sometimes he became the “inadvertent object of political leaders who choose to make me a symbol of all that they think is wrong and unpatriotic about Muslims in India”.
He wrote that he has been “accused of bearing allegiance to our neighbouring nation than my own country – this even though I am an Indian whose father fought for the freedom of India”.
Following the article, Pakistani Interior Minister Rehman Malik requested that India provide security for the actor.
India on Tuesday dismissed Mr Malik’s suggestion and advised him to look after the security of Pakistani citizens.
Reacting to Mr Malik’s remarks, Khan told reporters: “I would like to tell all those who are offering unsolicited advice that we in India are extremely safe and happy.
“We have an amazing democratic, free and secular way of life. In the environment that we live here in my country India, we have no safety issues regarding life and material. As a matter-of-fact, it is irksome for me to clarify this non-existent issue.”
Khan said many people were reacting to his article without reading it.
“Ironically, the article… was actually meant to reiterate that on some occasions my being an Indian Muslim film star is misused by bigots and narrow minded people who have misplaced religious ideologies for small gains… and ironically the same has happened through this article… once again,” he said.
Khan has appeared in more than 70 films, anchored TV shows and done innumerable advertisements.
He also owns the Kolkata Knight Riders team of the lucrative Indian Premier League cricket tournament.
Khan has family roots in the Pakistani city of Peshawar and has a huge fan following there too.