Khan, who is to meet Indian cricket board chief Jagmohan Dalmiya, was however later allowed to enter the city as a "special case" following intervention by the Union Home Ministry, sources said.
Although Khan has a valid visa, a Pakistani national can travel to India through one of the four routes approved by the Home Ministry--Delhi, Mumbai, Chennai and Attari (Amritsar).
Khan was stopped by the immigration officials at around 9.30 pm because he was entering India through Kolkata which was not an approved point of entry.