Khan's body was found by villagers in the North Waziristan town of Miran Shah, where he had been kidnapped six months earlier. Khan was abducted on December 5, 2005, by five gunmen who ran his car off the road as his younger brother, Haseenullah, watched helplessly. Local government officials and family members said Khan, 32, had been found handcuffed and shot several times. His body appeared frail and he had grown a long beard since he was last seen, Pakistani journalists told CPJ.
The day before his abduction, Khan photographed what apparently were the remnants of a U.S.-made missile said to have struck a house in Miran Shah on December 1, 2005, killing senior Al-Qaeda figure Hamza Rabia. The pictures, widely distributed by the European Pressphoto Agency on the day they were shot, contradicted the Pakistani government's explanation that Rabia had died in a blast caused by explosives within the house. International news media identified the fragments in the photographs as part of a Hellfire missile, possibly fired from a U.S. drone.
Khan, who was also a reporter for the Urdu-language daily Ausaf, had received numerous threats from Pakistani security forces, Taliban members, and local tribesmen because of his reporting.
During Khan's six-month disappearance, government officials provided his family with numerous and often contradictory accounts of his whereabouts: Khan was in government custody, soon to be released; Khan had been abducted by "miscreants"; he had been taken by Waziristan mujahideen; he had been flown to the military base at Rawalpindi and was then detained in Kohat air base.
Khan's relatives were told by hospital workers that he had five or six bullet wounds and that one hand had been manacled in handcuffs typically used by Pakistan's Inter-Services Intelligence Directorate. Mahmud Ali Durrani, Pakistan's ambassador to the United States, dismissed the reported presence of the handcuffs as circumstantial and said the cuffs could have been planted to incriminate the government. No autopsy was performed.
An investigation led by High Court Justice Mohammed Reza Khan was conducted, but the results were not made public. Hayatullah Khan's family said they were not interviewed by the judge or other investigators. North West Frontier Gov. Ali Mohammad Jan Orakzai told CPJ that North Waziristan was not secure enough to risk exposing a judicial figure to kidnapping or death. CPJ has repeatedly sought the release of the report, making a direct request to President Asif Ali Zardari in 2011. The report remained a secret as of February 2013.
In November 2007, Khan's widow was killed in a bomb that was detonated outside her home.