The Pakistani High Commission in Delhi, however, claimed today he had never applied for any visa application.
Kher was one of the 18 Indians invited to the four-day prestigious event by the organisers but he is the only one who has been denied the visa.
The other 17 Indian participants who have been given the travel document included senior Congress leader Salman Khurshid and actor Nandita Das.
The noted actor, who has just been honoured with Padma Bhushan by the government, today said he was very "sad and disappointed" over the matter and wondered whether he was denied visa for raising the issue of Kashmiri Pandits, supporting Prime Minister Narendra Modi and for being a patriot.
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When contacted, Pakistan High Commission's head of media Manzoor Memon said Kher had never submitted visa application to Pakistan High Commission. "So the question of issuing or denying him visa does not arise."
But the organizers of the annual Karachi Literature Festival (KLF) said they are unaware of the reasons for rejection of visa to the actor.
"That is all we have been told. They told us that the remaining 17 guests invited from India should be asked to submit applications as they would be issued visas," she said.
Kher was also denied a visa last year in May to visit Lahore on an invitation of a Pakistani NGO and security reasons were cited for the decision.
Rejecting Pakistan High Commission's contention that he had not applied for visa, Kher called it a "laughable explanation". He said organisers had completed the formalities for the visa.
Sources in the Pakistan government said in Karachi since
Kher is very much active and vocal in the social media on sensitive issues pertaining to religion and Indo-Pak relations he was not asked to submit his application.
The KLF spokesperson said around 35 invitees from abroad are participating in the festival including from the US, Britain and Bangladesh besides India.
"They are telling a lie. I do not have to do it. The organisers had done it," the actor said.
Kher said the visa denial has left the festival organisers embarrassed and they have apologised to him.
"We welcome their artistes in India. If there are objections to their performance at one place in India they are welcome at other places. But there is no reciprocity," he said.
KLF's Sayed felt the Bollywood star's presence would have given the Karachi audience a different perspective.
"We had organised an exclusive session for him with Ashok Chopra with a very large audience. People would have asked him questions about his views. He would have had a chance to talk to them, to engage with them, to answer their questions and in the process some understanding would have developed.