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".
Senior BJP leader Kailash Vijayvargiya has drawn strong criticism from his own party and others for his attack on Shah Rukh Khan over the film star's comments on religious intolerance.
"Shah Rukh Khan lives in India, but his heart is in Pakistan. His films make crores here but he finds India intolerant," the former Madhya Pradesh minister and BJP general secretary tweeted today.
"I condemn his comments outright," said union minister and BJP leader Prakash Javadekar, pointing out that Mr Vijayvargiya is not a BJP spokesperson and so does not speak for the party.
"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.
Delhi chief minister Arvind Kejriwal sent the actor a message of support."We r all proud of you.@iamsrk Hope your words help to make a tolerant, inclusive and progressive India (sic)," Mr Kejriwal tweeted.
Shah Rukh Khan had joined the debate swirling around "intolerance" on Monday, his 50th birthday, when he told NDTV that there was "nothing worse than religious intolerance and that it would take India to the Dark Ages".
"Our religion cannot be defined or showed respect to by our meat-eating habits. How banal and silly is that," said Shah Rukh Khan, supporting the many writers, filmmakers and others who have returned awards in protest after incidents of mob attacks over rumours of beef eating and cow slaughter and killings of noted rationalist writers.
"Isn't this treason? India is about to become a member of the United Nations Security Council. All forces opposing India including Pakistan are conspiring against it," Mr Vijayvargiya tweeted today responding to the comments made by Mr Khan.
"Creating an atmosphere of intolerance in India is part of the conspiracy. Shah Rukh's tune is to sing with Pakistan and these forces against India," he wrote.
"When hundreds were killed in Bombay in 1993, then where was Shah Rukh Khan? When Mumbai 26/11 attack was where Shah Rukh?" he said.
Mr Vijayvargiya added that the whole world today "values India and its leadership". "To talk of growing intolerance now would be weakening India before the world," he said.