Pakistan's high commission in India and foreign and interior ministries have been directed not to issue a Pakistani visa to Khan.
The Bollywood star, while attending a party at the premiere of the Indian film "Taj Mahal" in Lahore on April 26, had made controversial remarks.
"Pakistan was made in the name of Islam but look how the Muslims here are killing one another. Have you ever heard of a Hindu killing a Muslim in the secular state of India?" He was quoted as saying by the Pakistani media.
Khan had also got into a scuffle with Sakre Aalam who was anchoring the party.
Mahesh Bhatt, Pehlaj Nihlani and Shatrughan Sinha, all part of the Indian team at the party, had then apologised on Khan's behalf.
Later, Khan, however, said: "Believe me, I did not say anything against Pakistan. I am a Muslim and love Pakistan as much as I love India and that is why I am planning to shoot a movie in Pakistan in the near future which would be a co-production".
While Bollywood films and stars have a lot of fan following in the country, there has been a virtual ban since 1965 against release of Indian films here.
Pakistan, however, permitted Akbar Khan's 'Taj Mahal' and K. Asif's 'Mughal-E-Azam' to be released in the country last month.