The Afghan Taliban has accused Pakistan of violating Kabul's sovereign territory, describing it as an unprecedented, violent, and provocative act.
The allegation comes after two loud blasts were heard in the city late on Thursday.
Pakistan had also bombed a civilian market in the border province of Patika, in Afghanistan's south-east, the Taliban Defence Ministry said in a statement on Friday. Locals there told the BBC's Afghan service that a number of shops had been destroyed.
Pakistan has neither confirmed nor denied that they launched an attack inside Afghanistan.
However, during a press conference held in the city of Peshawar on Friday, a top general alleged Afghanistan was being used as a base of operation for terrorism against Pakistan. To safeguard Pakistani lives and properties, what measures need to be taken will be taken, General Ahmed Sharif Chaudhry added.
Pakistan has long accused the Afghan Taliban of permitting the Pakistan Taliban, also known as the TTP, to operate from their land. The Taliban government have always denied this.
Rumours had circulated that the blasts in Kabul were part of a targeted attack on the TTP's leader, Noor Wali Mehsud.
In response, the TTP released an unverified voice note from Mehsud saying he was still alive.
Exactly what happened is unclear; BBC Afghan's correspondent saw no signs of an explosion in the suspected location of the blasts on Friday, but did report a heavy Taliban presence and mobile checkpoints.
The Taliban Defence Ministry warned in its statement that, should the situation become worse, the consequences will be attributable to the Pakistani army.
However, the Taliban's foreign minister - who is currently in the Indian capital Delhi - said they wanted to maintain good relations with Pakistan. Pakistan should not repeat this mistake, Amir Khan Muttaqi told a select group of 16 male journalists from Indian media. Our issues can be solved by negotiation not by war.