One Afghan official said the attacks would be met with retaliation.
Pakistani security forces carried out a ground operation along the Pakistan-Afghanistan border late on Sunday, followed by strikes against militant hideouts and safe havens, killing 29 fighters, Pakistani Information Minister Attaullah Tarar said.
Pakistan said the operations were launched in response to multiple militant attacks across Pakistan.
Afghanistan condemned the strikes as a "cowardly act of aggression" and an "act of brutality".
Hayatullah Mohajer Farahi, the deputy minister for publications at the Ministry of Information and Culture, said Afghanistan would respond "in due time".
Hamdullah Fitrat, the deputy spokesman for Afghanistan's Taliban government, said the Pakistani forces targeted a home in Paktia's Chamkani district, killing an elderly man and a child, while other family members were wounded.
When residents gathered to rescue people, the area was struck again, killing 28 villagers and wounding 158, he said.
Six people, mostly women and children, were killed in a village in Giyan district, Paktika province, when another home was struck, he said.
A civilian home in Kunar province was also hit, causing no casualties but killing some 30 livestock.
Pakistani officials said an uneasy calm prevailed along the Pakistan‑Afghanistan border on Monday, with security forces remaining on high alert.
On Monday, Afghanistan and Pakistan summoned each other's top diplomats to protest the attacks.
Tarar, the Pakistani information minister, shared three videos on X that he said showed projectiles striking sprawling camps and safe havens of Jamaat-ul-Ahrar and Fitna al-Khwarij in Afghanistan's Paktia, Paktika and Kunar provinces.
Tarar said the overnight strikes killed "terrorists" and destroyed weapons and ammunition stockpiles.
He said Pakistan's relentless counter-terrorism campaign "will continue at full pace".
Jamaat-ul-Ahrar is a breakaway faction of the Pakistani Taliban.
Militant attacks targeting Pakistan's police and security forces have surged in recent years.
Authorities have blamed the Pakistani Taliban, or TTP, and allied militant groups for most of the violence.
The Pakistani Taliban are separate from but allied with the Afghan Taliban that returned to power in 2021.
The Pakistani security operation followed a militant attack targeting the regional headquarters of the paramilitary Rangers in Karachi that killed three soldiers.
Security forces killed three attackers and arrested another assailant, whom the military identified as a wounded Afghan national.
Jamaat-ul-Ahrar claimed responsibility for the Karachi attack.
Sunday's cross-border strikes and ground operation came less than three weeks after Pakistan's military launched air strikes on what it said were militant hideouts in Afghanistan.
They ended about a month of relative calm following what Islamabad had described as an "open war" between the neighbouring countries, despite international efforts to broker a lasting peace.
Hundreds of people have been killed in cross-border fighting since February, when Afghanistan launched retaliatory strikes after Pakistan carried out airstrikes inside Afghan territory.
