The hideouts in Pakistan's Balochistan and Khyber Pakhtunkhwa provinces, both of which share a border with Afghanistan, were targeted by the "air force" on Thursday night, the ministry said in a post on X. It did not specify how the attack – Kabul's first major offensive action in months – was carried out.
Afghanistan has no fighter jets but is known to possess at least six aircraft and 23 helicopters, according to data from the London-based International Institute for Strategic Studies, Reuters reported.
The Taliban forces are also known to have drones that have been used in fighting with Pakistan.
"These bases, allegedly used in cooperation with certain hostile intelligence circles to plan and organize attacks against Afghanistan, had previously served as staging grounds for several deadly attacks," it said.
"According to preliminary information, the operation successfully hit its key pre-designated targets," it added, without giving details about casualties.
Pakistan's military and information ministry did not immediately respond to requests for comment.
The conflict between Pakistan and Afghanistan has killed hundreds of people this year, with efforts to ease tensions, mediated by China, yielding no results so far.
Islamabad has blamed Kabul for harboring militants that it says plot attacks in Pakistan, but the Afghan Taliban deny the allegations and says militancy is Pakistan's internal problem.
Pakistan launched air strikes on Afghan provinces last week, which the Afghan Taliban said killed at least 13 people, including 11 children, and injured 14.
Islamabad said the "calibrated strikes" killed 26 militants and were a response to a recent spate of attacks in the country's northwest.
"Afghanistan will no longer tolerate any threat to its security and stability. It will use all available means and capabilities to neutralize and eliminate any threat at its source," the Afghan Taliban defense ministry said.