Police Chief Abdul Rahman Sarjang said Mohammad Ali Jalali's body was recovered today from a desert area in Ghazni Province.
Jalali and four others were abducted from a car on May 21 after attending a funeral service in the town of Chahar Diwar in Ghazni.
Sarjang said the other abductees were released alive.
A purported Taliban spokesman, Qari Yosuf Ahmadi, says Taliban fighters killed the former governor.
Jalali was a respected tribal leader in Paktika, a volatile province that borders Pakistan. He was also the first governor that Karzai appointed in the province after the ouster of the Taliban regime in late 2001.