Last week the Afghan government banned "Kabul Express" from being screened in the country as portions of the movie were said to portray the minority Hazara community as thieves.
"The film has some quotes that are derogatory and offensive towards the Hazara ethnic group," minister of culture advisor Najib Manalai told reporters in Kabul.
The Shiite Hazara community makes up about 10 percent of the Afghan population and have been the victims of persecution by rival ethnic and religious groups in Afghanistan.
Khan declined to comment on whether derogatory language was used in the movie, which took 45 days to film in Afghanistan last year under strict security conditions.
The film opened in late December in India to mixed reviews and small box office success.
The story revolves around two Indian journalists after the US-led invasion in 2001 who aim to interview Taliban leaders.
Khan brings together Pakistani actor Salman Shahid, Indians John Abraham and Arshad Warsi, Afghan actor Hanif Hum Ghum and American actress Linda Arsenio.
In the film, they are forced to trust each other during a kidnap ordeal spread over two days.
Life in Afghanistan has long had a powerful appeal in India. In return, Bollywood flicks have a huge fan base in the war-torn country.