Two Apache helicopters from the International Security Assistance Force (Isaf) in Afghanistan are said to have taken part in the weekend's operation.
It followed an attack by insurgents on an Afghan security outpost in Khost.
Isaf said no civilians were killed in the operation, but this has not been independently confirmed.
The BBC's Ian Pannell in the Afghan capital, Kabul, says that although manned military raids over the border are not unprecedented, it will no doubt prove controversial in Pakistan.
In a statement, Isaf said Afghan forces in the eastern province of Khost were attacked on Friday by "a significant number of insurgents".
"An air team in the area observed the enemy fire, and following International Security Assistance Force rules of engagement, crossed into the area of enemy fire."
Isaf told the BBC its aircraft killed 49 insurgents.
On Saturday, two Apache helicopters came under small-arms fire from the same area and again crossed the border, killing four to six insurgents, said Isaf.
Pakistani media said fighters from the Haqqani network, a branch of the Afghan Taliban which operates in Pakistan, died in the Nato air raids.
An Isaf spokesman, Sgt Matt Summers, confirmed the helicopters had crossed into Pakistan.
But he did not reveal the location of the operation or say which Isaf countries' forces were involved.
American forces regularly use drone aircraft for missile strikes in Pakistan's tribal belt, but manned air raids across the border are rare.
Isaf's force was established by the UN in late 2001 with a stated mission of promoting security and development; it is also training Afghan soldiers and police.
The BBC's Ian Pannell in the Afghan capital, Kabul, says that although manned military raids over the border are not unprecedented, it will no doubt prove controversial in Pakistan.
In a statement, Isaf said Afghan forces in the eastern province of Khost were attacked on Friday by "a significant number of insurgents".
"An air team in the area observed the enemy fire, and following International Security Assistance Force rules of engagement, crossed into the area of enemy fire."
Isaf told the BBC its aircraft killed 49 insurgents.
On Saturday, two Apache helicopters came under small-arms fire from the same area and again crossed the border, killing four to six insurgents, said Isaf.
Pakistani media said fighters from the Haqqani network, a branch of the Afghan Taliban which operates in Pakistan, died in the Nato air raids.
An Isaf spokesman, Sgt Matt Summers, confirmed the helicopters had crossed into Pakistan.
But he did not reveal the location of the operation or say which Isaf countries' forces were involved.
American forces regularly use drone aircraft for missile strikes in Pakistan's tribal belt, but manned air raids across the border are rare.
Isaf's force was established by the UN in late 2001 with a stated mission of promoting security and development; it is also training Afghan soldiers and police.
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