Pakistan's government dismissed the reports as "continuous propaganda".
About 30 students, women and children were among those wounded in the attacks, which targeted homes and the Syed Jamaluddin Afghani University in Kunar province's Asadabad, the Taliban's deputy spokesperson Hamdullah Fitrat said.
"We strongly condemn these attacks by the Pakistani military regime, in which ordinary people, academic, and educational institutions were targeted, and declare them unforgivable war crimes," he said in a post on X.
Pakistan's information ministry in a post on X said the Afghan government's allegations were false.
"Whenever and wherever Pakistan strikes the Afghan-based terror infrastructure, it will be as per previous actions, well declared, fully owned and backed by precise evidence of targeting terror support infrastructure," it said.
The Pakistani military did not immediately respond to a request for comment.
The worst fighting in years erupted between the allies-turned-foes in February, with Pakistani air strikes inside Afghanistan that Islamabad said targeted militant strongholds.
Islamabad has said Kabul provides safe haven to militants executing attacks on Pakistan from its soil. The Taliban has denied the allegations and said militancy in Pakistan is an internal problem.
More than 400 people were killed in a Pakistani strike on a drug rehabilitation centre in Kabul last month, the Taliban had said, before the neighbours suspended fighting.
The United Nations Assistance Mission in Afghanistan had put the death toll at 143.
China, which was mediating between the countries, said earlier this month that they had agreed during peace talks in Urumqi to explore a comprehensive solution to their conflict.
Skirmishes have died down since the talks in Urumqi were announced, but there have been reports of a few small clashes. Three people were killed in mortar shelling by Afghan forces on April 18 in Pakistan's northern Bajaur region, security officials said.
