Two Pakistani diplomats based in a consulate office in the eastern Afghan city of Jalalabad have been missing since Friday, when they set off by road back to their homeland, Pakistan's foreign office said on Sunday.
Islamabad did not speculate who may be behind the disappearances but various Afghanistan-based Islamist groups have targeted diplomats in the past.
"Pakistan has requested the Afghan Government that all efforts may be made to ensure early recovery of our officials and bring the perpetrators of this heinous crime to justice," the foreign ministry said in a statement
Islamabad said Afghanistan had formed three different investigating groups to probe the incident.
Relations between Islamabad and Kabul have been tense in recent years, with both countries accusing each other of not doing enough to tackle Pakistani and Afghan Taliban militants.
Afghanistan has accused Pakistan of turning a blind eye to Afghan Taliban commanders based within its borders and of supporting the militant group, something Islamabad denies.
Islamabad has claimed that Kabul is not doing enough to tackle Pakistani Taliban militants who have been driven out of Pakistan, but who still carry out attacks across the border.
Jalalabad, the provincial capital of Nangarhar province, is a busy trading hub about 70 kilometres (43 miles) from the main border crossing with Pakistan, from which landlocked Afghanistan imports much of its goods.
The province is home to various Islamist groups, including Pakistani and Afghan Taliban. In recent years DAESH has also established a presence Nangarhar.