On September 28, 2002, Khan was arrested for rash and negligent driving after his car ran into a bakery in Mumbai; one person who was sleeping on the pavement outside the bakery died and three others were injured in the mishap.

On July 24, 2013, he was formally charged with culpable homicide in the case, to which he pleaded not guilty. On May 6, 2015, Khan was found guilty of all charges in the case. However, in December 2015, Khan was acquitted of all charges in this case, due to lack of evidence.

On February 17, 2006, Khan was sentenced to one year in prison for hunting black buck, an endangered deer species. The sentence was stayed by a higher court during appeal. On April 10, 2006, he was handed a five-year jail term and remanded to Jodhpur jail until April 13 when he was granted bail.

On July 24, 2012, the Rajasthan High Court finalised charges against Khan and his colleagues in the black buck killing case, paving the way for start of the trial. Khan was acquitted in the case by the Rajasthan High Court on July 24, 2016.

In a related case registered under the Arms Act, Khan was on January 18, 2017 acquitted of all charges, as he was found “not guilty” of keeping an unlicensed weapon and using it for hunting.