Promotional footage for the feature has been banned in India's neighbouring country because of its representation of Pakistan's intelligence service.
Khan told followers on Twitter: "I will say it once more. Ek Tha Tiger is NOT anti Pakistan. In this day and age, it's stupid to make films that are insensitive or derogatory to any country or community.
"This is the price we have to pay because unfortunately our industry has made insensitive and jingoistic films in the past."
He added: "I am absolutely sure that once the censor board of Pakistan sees Ek Tha Tiger, they will be more than happy to show the film in Pakistan.
"I can assure the millions of fans of Salman [Khan] in Pakistan that Ek Tha Tiger will release in theatres in their country."
Khan has previously said that the film's co-stars Salman Khan and Katrina Kaif look "magical" together.
Kaif revealed in March that she loved doing her own stunts for the action film, where she plays a dance instructor.
Watch the trailer for Ek Tha Tiger below: