Government spokesman Zabihullah Mujahid said on X that Pakistan's aircraft also struck fuel depots belonging to the private airline Kam Air near Kandahar airport.
"This company supplies fuel to civilian airlines as well as to United Nations aircraft," he said on Friday.
Pakistan's military and government did not immediately comment.
Pakistan and Afghanistan have been targeting each other's military installations since late February, when Kabul said it struck Pakistani posts in response to Pakistani attacks along the border.
Pakistan's military has said its operations targeted the Pakistani Taliban and their support networks along the border, which Afghanistan has never formally recognised.
Both sides have claimed to inflict heavy losses in what has become their deadliest fighting in years, a confrontation Islamabad has described as an "open war" with Afghanistan.
In his posts on X, Mujahid claimed that Pakistani strikes hit civilian sites and uninhabited locations in Afghanistan's Paktia and Paktika provinces, as well as other areas.
He said the attacks "will not go unanswered".
Kabul police spokesman Khalid Zadran said at least four civilians, including children, were killed in the city and 15 others were injured.
The latest Pakistani strikes came a day after China's special envoy, Yue Xiaoyong, arrived in Islamabad and met with his Pakistani counterpart, Mohammad Sadiq, following a visit to Kabul where he met Afghan government officials.
Sadiq, Pakistan's special envoy for Afghanistan, wrote on X the previous day that he and Yue "discussed threats posed by terrorist groups such as TTP and ETIM (East Turkestan Islamic Movement) to Pakistan and China respectively" and agreed on the need for collective efforts to ensure lasting peace and stability.
Repeated calls from the international community for restraint have had little effect.
Pakistan has previously said its strikes along the border and inside Afghanistan are aimed solely at Khawarij, a phrase Islamabad uses for the outlawed Pakistani Taliban, also known as Tehrik-e-Taliban Pakistan, or TTP.
Islamabad frequently accuses Afghanistan's Taliban government of harbouring the group, a charge Kabul denies.
