Sir Salman spent a decade in hiding after the Iranian spiritual leader Ayatollah Ruhollah Khomeini issued a fatwa in 1989 calling for his death.
He was forced to pull out of an appearance at the Jaipur Literary Festival in January amid threats of violence.
Mr Khan said he stood by his decision not to appear alongside the author and that there were limits to free speech.
“The Koran is a way of life,” he said. “So when anyone attacks that, it causes immense pain to us. So whatever causes pain to such a large part of humanity, you should lay off the subject.”
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