"If there was intolerance in India, then after Amitabh Bachchan, Shah Rukh Khan would not have been the most popular actor. My tweets have been misinterpreted by some people.
"My motive was not to hurt anyone. I retract my tweets," Vijayvargiya posted on his Twitter page.
On Tuesday, he made headlines when he took to the social media platform and posted a message in five tweets.
He wrote that while Shah Rukh stays in India, his heart and mind are always in Pakistan, and that while his films make millions in India, the 50-year-old actor still finds "extreme intolerance" in the country.
"If this is not being a traitor, then what's it? India is to become a permanent member of the UN Security Council. Countries opposed to India, including Pakistan, are conspiring against it. "Creating an environment of intolerance is part of the conspiracy. Shah Rukh has been singing the song of intolerance, which is in tune with Pakistan and other countries opposed to India.
"When many people were killed in the 1993 bomb blasts in Mumbai, then where was Shah Rukh Khan? When 26/11 happened in Mumbai, where was he? Today, the entire world is lauding the leadership of India. And to talk of growing intolerance in such an environment, will weaken India's stature in the world."
SRK had earlier made a comment to a TV channel on his 50th birthday, and said that "There is intolerance, there is extreme intolerance, there is, I think... there is growing intolerance".