According to a report on ESPNcricinfo, Khan also has allegedly threatened the umpire and questioned his decision while going on to abandon the team in protest at the charges laid against him.
Khan was supposed to attend a hearing conducted by the match referee but the 38-year-old was not available as he had already left for his native city Karachi.
In the absence of Khan, the Khyber Pakhtunkhwa team will be captained by Ahmed Shehzad for the rest of the tournament.
Khyber Pakhtunkhwa have participated in two games in the Pakistan Cup thus far and have lost one match against Islamabad while winning the match against Punjab.
In the first match against Islamabad, Khan hit a 59-ball 61 which was laced with six fours and a six while he scored just two runs before being run out in the second game against Punjab.
© Cricket World 2016