Mullah Mohammad Yaqoob told reporters at a news conference in Kabul that American drones have been entering Afghanistan via Pakistan.
"According to our information the drones are entering through Pakistan to Afghanistan, they use Pakistan's airspace, we ask Pakistan, don't use your airspace against us," he said.
Pakistan's foreign ministry did not immediately respond to a request for comment. Pakistani authorities have denied involvement in or advanced knowledge of a drone strike the United States said it carried out in Kabul in July that killed al Qaeda leader Ayman al-Zawahiri.
Yaqoob's comments could exacerbate tension between the neighbouring nations at a time when the Afghan Taliban is mediating talks between Pakistan and a Pakistani Taliban militant group.
Afghanistan also relies heavily on trade with Pakistan as the country experiences an economic crisis.
The Taliban said that it is investigating the July air strike and that it has not found the Al Qaeda leader's body.