Foreign Secretary Aizaz Ahmad Chaudhary summoned Afghan ambassador to Pakistan Hazrat Omar Zakhilwal and lodged "strong protest" over the killing of Major Ali Jawad Khan, Foreign Office (FO) said in a statement.
Khan was injured on June 13 due to the "unprovoked firing" by Afghan security forces over the contentious fencing issue at north-western Torkham border crossing. He died of injuries yesterday.
FO also asked Afghanistan to take immediate steps to bring the unprovoked firing to an end.
Chaudhary expressed concern over the continued firing by the Afghan forces for last few days with a view to disrupt the construction works aimed at strengthening effective border management.
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He rejected allegations of Afghanistan that the construction work being undertaken by Pakistan was violation of the agreements and understandings reached between the two countries.
It was reiterated that these works are being undertaken on Pakistani side and were started after the two sides had agreed on them during the meetings held last month.
In the firing between security forces, an Afghan border guard was killed while two Pakistani soldiers and nine civilians were injured. One of the injured soldiers has died.
Pakistan alleged that "unprovoked" firing was started by Afghanistan's security forces when construction work began on a new gate on the Pakistani side.
Last month, the border crossing was sealed for several days over the construction of the gate, causing hardships to thousands of people who cross it every day.