In a series of five tweets Mr Vijayvargiya also accused Mr Khan of "treason" and being part of a "conspiracy to create an atmosphere of intolerance in India".
After triggering outrage with his five-tweet attack on Shah Rukh Khan, senior BJP leader Kailash Vijayvargiya retracted his comments on Wednesday morning and said they had been "misunderstood."
"Shah Rukh Khan lives in India, but his heart is in Pakistan. His films make crores here but he finds India intolerant," Mr Vijayvargiya had tweeted on Tuesday, drawing severe criticism, also by his own party.
He had also tweeted, "When many died in Bombay in 1993, where was Shah Rukh Khan? When 26/11 attacks took place in Mumbai, where was Shah Rukh?", a reaction to Shah Rukh Khan's remark that there is much intolerance in the country.
"I condemn his comments outright," said union minister and BJP leader Prakash Javadekar soon after, pointing out that Mr Vijayvargiya is not a BJP spokesperson and so does not speak for the party.
Senior minister M Venkaiah Naidu said this morning that he had not seen Mr Vijayvargiya's remarks, but asserted, "It is not view of the party. We all admire Shah Rukh Khan."
On Wednesday the BJP general secretary tried damage control. "I didn't intend to hurt anyone. I take back my tweets," Mr Vijayvargiya, 59, tweeted and also, "Shah Rukh wouldn't have been the most popular actor after Amitabh (Bachchan) had India been intolerant. My tweets were misunderstood by some."
There were few takers for the almost apology. The Congress has demand Mr Vijayvargiya's arrest and that of another BJP leader Yogi Aditynath who added to his party's acute embarrassment by comparing Shah Rukh Khan to 26/11 terror mastermind Hafiz Saeed.
#KailashVijayvargiyaLeaveIndia trended worldwide on Twitter on Wednesday as the actor's fans tore into the BJP leader.
Other parties also slammed him. "Sickening remarks against @iamsrk by BJP national gen sec also in charge of Bengal.What attitude is this: everyone is bad & only u r good? (sic)" tweeted Trinamool Congress leader Derek O'Brien.
Shah Rukh Khan had, on Monday, his 50th birthday, said, "Religious intolerance, or intolerance of any kind, is the worst thing and will take us to the dark ages."