Pakistan summoned the senior diplomat to protest what it described as "unprovoked firing" by Afghan border forces at a Pakistani check post, the second such incident within a week.
The Afghan Charge d'Affaires was "summoned to the Foreign Office today for conveying the protest of the Government of Pakistan on repetition of an unprovoked firing incident that took place on May 6, 2013 at 0845 hours from the Afghan posts on the Pakistani Gursal post", said a statement from the Foreign Office spokesman.
Five soldiers of Pakistan's Frontier Constabulary were injured in the incident of firing yesterday, the statement said.
"As in the past, Pakistan security forces exercised maximum restraint and communicated first to the Afghan side about repetition of this serious violation through military channels," it said.
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The Afghan Charge d'Affaires was informed about Pakistan's "serious concern and asked to advise the relevant authorities in Afghanistan to avoid repetition of unprovoked firing which undermines the existing coordination mechanisms" between troops of both sides.
"The repetition of unprovoked firing incidents are adversely affecting the friendly relations between the two brotherly countries, which have covered a long distance in building trust and understanding in recent years", the statement said.
Yesterday's clash occurred after Afghan President Hamid Karzai said his government would never recognise the current border with Pakistan.
Afghan grievances over the frontier with Pakistan date back to the drawing of the Durand Line by Britain in 1893.
The Governor of Afghanistan's Nangarhar province said several Pakistani border check posts had been torn down.
The Afghan Foreign Ministry summoned the Pakistani Charge d'Affaires yesterday to lodge a "strong protest" over the latest violence.
The ministry said Pakistan would "bear responsibility for any consequences" if it refused to move Pakistani posts in areas which Afghanistan says are within its territory.