Gulbuddin Hekmatyar, named as a global terrorist by the US, also claimed the helicopter pilot wants to "kill innocent Afghans while drunk", The Sun reported.
Harry has been flying Apache choppers in Helmand province.
"The British prince wants to hunt down mujahideen with his helicopter rockets without any shame. But he does not understand the hunting of Afghan lions and eagles is not that easy. Jackals cannot hunt lions," Hekmatyar was quoted as saying.
The Afghan leader also referred to a failed Taliban attack on Britain's Camp Bastion military base in September.
"The prince (Harry) saw that he was the one about to be hunted and was searching for a hole in which to hide himself," he said.