Pakistan's ambassador to Kabul, was summoned to lodge a formal complaint, the ministry said.
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.