Pakistani troops have fired shots into the air to stop US troops crossing into the South Waziristan region of Pakistan, local officials say.
Reports say nine US helicopters landed on the Afghan side of the border and US troops then tried to cross the border.
South Waziristan is one of the main areas from which Islamist militants launch attacks into Afghanistan.
The incident comes amid growing anger in Pakistan over increasingly aggressive US attacks along the border.
The latest confrontation began at around midnight, local people say.
They say seven US helicopter gunships and two troop-carrying Chinook helicopters landed in the Afghan province of Paktika near the Zohba mountain range.
US troops from the Chinooks then tried to cross the border. As they did so, Pakistani paramilitary soldiers at a checkpoint opened fire into the air and the US troops decided not to continue forward, local Pakistani officials say.
Reports say the firing lasted for several hours. Local people evacuated their homes and tribesmen took up defensive positions in the mountains.
The incident happened close to the town of Angoor Adda, some 30km (20 miles) from Wana, the main town of South Waziristan.
A Pakistani military spokesman in Islamabad confirmed that there was firing but denied that Pakistani troops were involved.
It emerged last week that US President George W Bush has in recent months authorised military raids against militants inside Pakistan without prior approval from Islamabad.
The BBC's Barbara Plett in Islamabad says there is a growing American conviction that Pakistan is either unwilling or unable to eliminate militant sanctuaries in its border area.
There have been a number of missile attacks aimed at militants in Pakistan territory in recent weeks.
Pakistan reacted with diplomatic fury when US helicopters landed troops in South Waziristan on 3 September. It was the first ground assault by US troops in Pakistan.
Locals in the Musa Nikeh area said American soldiers attacked a target with gunfire and bombs, and said women and children were among some 20 civilians who died in the attack.
In the latest incident, the tribesmen say they grabbed their guns and took up defensive positions after placing their women and children out of harm's way.
Pakistan's army has warned that the aggressive US policy will widen the insurgency by uniting the tribesmen with the Taleban.
Last week the army chief declared that Pakistan would defend the country's territorial integrity at all cost, although the prime minister has since said this would have to be through diplomatic channels rather than military retaliation.