“Our troops did not spare them, opened fire on them and they turned away,” a Pakistani security official said in confirming the incident.
Other sources noted that US armoured vehicles were seen moving on the Afghan side of the border.
Pakistan Military spokesman Major Murad Khan confirmed that shooting had taken place, but said that US helicopters did not cross into Pakistani airspace and Pakistani troops were not responsible for the shooting.
On 3 September at least 20 people, including women and children, were killed in Angoor Adda, sparking outrage in Pakistan, prompting a diplomatic protest.
The New York Times newspaper reported last week that US President George W. Bush gave the green light for US raids across the border.
The latest episode was the first overt ground incursion by US troops into Pakistan since US forces went into Afghanistan in 2001.
In the past few weeks the United States has intensified attacks by missile-firing drone aircraft on suspected al-Qaeda and Taliban targets in Pakistan’s tribal areas.
Pakistan is a crucial US ally in its war on terrorism, and its support is key to the success of Western forces trying to stabilize Afghanistan. But Washington has become impatient over Islamabad's response to the threat from al-Qaeda and Taliban fighters in Pakistan's tribal lands along the border.
Last week Pakistani Army Chief General Ashfaq Kayani said that Pakistan would not allow foreign troops onto its soil and Pakistan's sovereignty and territorial integrity would be defended at all costs.