The attack underscored distrust between the two countries that has deepened since they became allies in the US-led "war on terror" after the attacks on Sept 11, 2001.
The strike, which occurred late on Tuesday night, followed a clash between Afghan forces and Taliban militants in Kunar near the Pakistani Mohmand tribal area. Pakistan's prime minister, Yusuf Raza Gilani, condemned the attack.
"The senseless use of air power against a Pakistani border post by coalition forces is totally unacceptable. It constitutes a blatant and wilful negation of the huge sacrifices that Pakistan has made in its endeavour to combat terrorism," said a Pakistani foreign ministry statement.
A Pakistan army statement said the incident was a "completely unprovoked and cowardly act".
Maj Gen Athar Abbas, the chief army spokesman, said that 30-40 Afghan soldiers had tried to set up a post on a height above a Pakistani base in a "disputed area, a no-man's land".
The Afghans were persuaded to return "amicably", said the general, but were engaged by insurgents one mile inside Afghan territory.
He said that coalition air support provided to the Afghans targeted a nearby post housing members of the Pakistani paramilitary Frontier Corps.
"We believe it was a deliberate act of aggression," said Maj Gen Abbas.
A US military statement said that the air and artillery raid was aimed at Taliban militants and had been "co-ordinated with Pakistan".
Communications between Afghan and American forces and their Pakistani counterparts are remarkably poor.
US officials have expressed concern that the Pakistani policy of striking peace deals with militants has led to a tripling of cross-border infiltration by militants from Pakistan, particularly from Mohmand and neighbouring Bajaur.
Ahmed Rashid, a respected author and authority on the Taliban, said that American military chiefs are furious because the Pakistani army is withdrawing from the tribal areas.
"The bulk of the Pakistan army will remain deployed on its eastern border and train for any possible threats from its traditional enemy, India," he said.
"There are also signs that Washington is delaying delivery of US arms meant for the eastern front and is asking Western allies to do the same," he added.
The United States has used unmanned drones to attack suspected militants inside Pakistan.
Pakistan has protested over a series of missile strikes attributed to US-led forces in Afghanistan in recent months, including one in the tribal region of Bajaur in May that killed more than a dozen people.
Disputes over the 1,500-mile frontier between Pakistan and Afghanistan have been provoked by previous US strikes on Pakistani border posts.
The attack came two days after the Rand Corporation, a US Republican Party think tank, said in a report that members of Pakistan's intelligence services and its paramilitaries were supporting Taliban insurgents.
In: Afghanistan, News, Middle East
Tags: pakistan, afghanistan, friendly, fire, air, raid, tensions, rise
Location: Kunar, Balochistan, Pakistan (load item map)
Marked as: approved
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