The strikes were the latest spike in hostilities on the frontier between Afghanistan and Pakistan, with tensions escalating since the Taliban seized power in 2021.
Taliban government spokesman Zabihullah Mujahid told AFP that late on Tuesday Pakistan bombarded four areas in the Barmal district of eastern Paktika province.
"The total number of dead is 46, most of whom were children and women," he said, adding that six more people were wounded, mostly children.
Neither Pakistan's foreign ministry nor its military have responded to a request for comment.
But a senior Pakistan security official said the strikes were on "terrorist hideouts" using jets and drones and that they killed at least 20 militants from the Tehreek-e-Taliban Pakistan (TTP), the country's homegrown Taliban group.
"Arguments from Afghan officials claiming civilians are being harmed are baseless and misleading," he added, speaking on condition of anonymity.
A Taliban defence ministry statement late Tuesday condemned the strikes, calling them "barbaric" and a "clear aggression".
"The Islamic Emirate will not leave this cowardly act unanswered, but rather considers the defence of its territory and sovereignty to be its inalienable right," the statement said, using the Taliban authorities' name for the government.
Skirmishes on the frontier followed deadly air strikes in March by Pakistan's military in the border regions of Afghanistan, which Taliban authorities said killed eight civilians.
A Barmal resident, Maleel, told AFP Tuesday's strikes killed 18 members of one family.
"The bombardment hit two or three houses, in one house, 18 people were killed, the whole family lost their lives," he said.
He said a strike killed three people in another house and wounded several others, who were taken to hospital.
'Strikes will continue'
Taliban officials said the dead were local residents and people who had fled over the Pakistan border from the Waziristan region.
North Waziristan, which borders Paktika, has historically been a hive of militancy and was the target of a long-running Pakistani military offensive and US drone strikes during the post-9/11 occupation of Afghanistan that saw many people flee over the border.
The TTP in a statement on the strike claimed Pakistan "deliberately targeted refugee residences".
The strike comes after the TTP -- who share a common ideology with their Afghan counterparts -- last week claimed a raid on an army outpost near the border with Afghanistan, which Pakistan said killed 16 soldiers.
The Pakistani security official said the recent attack "was a significant trigger" for Tuesday's strikes, "but not the only one".
"The interim Taliban regime has been repeatedly urged to take action against the TTP, but their response has been lukewarm," he said. "Such strikes will continue as necessary."
Pakistan has been battling a resurgence of militant violence in its western border regions since the Taliban's 2021 return to power in Afghanistan.
Islamabad has accused Kabul's Taliban authorities of harbouring militant fighters, allowing them to strike on Pakistani soil with impunity.
Kabul has denied the allegations and pledged to evict foreign militant groups from Afghan soil.
But a UN Security Council report in July estimated up to 6,500 TTP fighters are based there -- and said "the Taliban do not conceive of TTP as a terrorist group".
The spike in attacks has soured Islamabad-Kabul relations. Security was cited as one reason for Pakistan's campaign last year to evict hundreds of thousands of undocumented Afghan migrants.
Earlier Tuesday, high-level Taliban officials were meeting with Pakistan's special envoy for Afghanistan who was on a visit to Kabul.
