The two sides have clashed previously on the border
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Pakistani troops have exchanged fire with Afghan soldiers across their common border in the latest in a series of similar incidents this week.
A Pakistani military official said mortars and small arms were used in the overnight clash.
No casualties were reported in the skirmish across the line dividing the Pakistani tribal region of Kurram from Paktia province in Afghanistan.
The two countries share a mountainous 2,640km-long border.
On Sunday, at least three people were killed after Pakistani and Afghan forces traded fire on the border.
At a meeting later to discuss the fighting, a US soldier and a Pakistani soldier were shot dead in disputed circumstances.
Both sides accuse each other of trying to establish posts on a disputed hilltop in the Terimangal area in the border region.
Reports say four Afghan troops and a Pakistani soldier have been injured in the latest clashes.
The governor of Afghanistan's Paktia province told the Associated Press that his border police told him that Pakistani forces began firing mortars at their positions early on Wednesday.
"I told my police forces, be patient and tolerant, because fighting is not the solution," Governor Rahmatullah Rahmat said.
'Disputed'
Last month, Afghan troops tore down part of a new anti-Taleban fence being erected by Pakistan on the border between the two countries.
Afghan officials had said the move led to fighting between Afghan and Pakistani troops. Pakistan had denied the fence claim, saying the clashes had started after one of its patrols came under fire.
Afghanistan disputes the border between the two countries - known as the Durand Line - saying it cuts off part of its territory.
The Durand Line was drawn up in 1893 by the colonial British administration in India. It left the powerful Pashtun tribes split between Pakistan and Afghanistan.