In a statement released late on Sunday, Pakistan’s foreign ministry said the incident was being investigated “at the highest level”.
Pakistan’s Foreign Secretary Sohail Mahmood, the top bureaucrat at the ministry, met with Afghanistan’s ambassador to Pakistan, Najib Alikhil, on Sunday, the statement said.
“We hope that the Government of Afghanistan would reconsider its decision.”
Earlier on Sunday, the Afghan government announced its decision to withdraw the ambassador and other senior diplomats from the Pakistani capital Islamabad.
The move came after a “strong protest” was lodged with Pakistan’s ambassador in Kabul, Mansoor Ahmad Khan.
Silsila Alikhil, the Afghan ambassador’s daughter, was abducted for several hours and “severely tortured” by unidentified attackers on Friday, Afghanistan’s government says.
On Sunday, however, Pakistan’s interior minister appeared sceptical of the Afghan government’s version of events.
“She was not kidnapped, we have simply registered a case in which [she] says she was kidnapped,” Interior Minister Sheikh Rashid Ahmed told Pakistani television news channel Geo News.
Ahmed said that Pakistani authorities had traced Alikhil’s phone to at least four locations, where security camera footage showed her boarding several taxis. He said that the owners or drivers of at least three taxis were in Pakistani custody.
Ahmed also alleged that Alikhil had deleted the contents of her mobile phone before handing it over to authorities during the investigation.
The incident has come as a fresh blow to relations between the South Asian neighbours, between whom tensions have risen in recent weeks.
Top Afghan officials, including Afghan President Ashraf Ghani, have accused Pakistan of supporting the Afghan Taliban in its armed push against the Afghan government.
Pakistan has denied the accusation, with Prime Minister Imran Khan reiterating in a meeting with Ghani on Friday that “instability and conflict were not in Pakistan’s interest”.