"After being released from the kidnappers' captivity, Alikhil is under medical care at the hospital," it added, urging an investigation and protection for Afghan diplomats.
A medical examination report, shared on social media and confirmed by the Pakistan Institute of Medical Sciences state hospital where Alikhil was treated, said she was admitted with swelling and rope marks on the wrists and ankles.
The report gave her age as 26, said she was held for more than five hours and also noted she had some swelling in the brain's rear occipital region.
Amid widespread consternation over the case in both nations, Afghan authorities summoned Pakistan's ambassador to Kabul to lodge a formal complaint.
Pakistan's foreign ministry said in a statement that the Afghan embassy had informed it Alikhil was assaulted while riding in a rented vehicle. Police were investigating the "disturbing incident" and security had been tightened for the ambassador and his family, it said.
Pakistani prime minister Imran Khan wanted the matter treated as top priority and the culprits caught within 48 hours, interior minister Sheikh Rashid Ahmed said.
Neighbours Pakistan and Afghanistan have long had frosty ties. Kabul accuses Pakistan of allowing safe havens for Taliban insurgents, while Islamabad accuses Kabul of allowing militants to use their territory to carry out attacks in Pakistan.
Both deny the charges.