Pakistani soldiers fired into the air to stop U.S. troops from entering South Waziristan from Afghanistan's Paktika province.
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.
The U.S. has been increasingly aggressive in recent weeks. Its troops did cross the border on Sept. 3. The pace of Predator drone-launched missile attacks within Pakistan seems to have grown in recent weeks.
This increased aggressiveness may come at a cost. From Monday's Globe and Mail:
The new U.S. strategy of unilateral attack against suspected militants inside Pakistani territory is threatening to send moderate Pakistani tribesmen to go fight alongside extremists against coalition forces in neighbouring Afghanistan.
The move piles more pressure on the fragile new democratic government in Islamabad, which is struggling to defend Pakistan's role in the war on terror against a hostile public that sees U.S. aggression as being as much of a danger as the Islamic militants.
Over the weekend, tribal chiefs in North Waziristan, the part of Pakistan's tribal borderland that was struck by the most recent civilian-killing U.S. missile attack, vowed to take the fight to Afghanistan if the United States does not halt attacks into Pakistan. These community leaders, representing the majority of people in North Waziristan, had not previously supported the extremists, but they are fiercely independent, armed and willing to fight anyone who trespasses on their land. Their anger could easily spread to other six other "agencies" that make up the tribal belt, several of which have also been subject to U.S. attacks.
There has been an intensified bombardment of the tribal territory with U.S. missile strikes against suspected Taliban and al-Qaeda training camps and hideouts, compounded by the first U.S. ground raid into the area earlier this month, apparently in exasperation at Pakistan's inaction. ...
During the past month, there have been seven U.S. missile strikes in the tribal area, about the same number as the whole of last year, representing a huge escalation in American intervention in Pakistan. The ground assault, which took place in South Waziristan, provoked a sharp rebuke from the Pakistan army, which is otherwise an ally in the "war on terror." Washington believes that Taliban and al-Qaeda militants fighting the U.S.-led coalition in Afghanistan use Pakistan's tribal area as a safe haven.
"If the Americans are coming to sort it out with force, they would create more enemies," said Ayaz Wazir, a retired Pakistani diplomat who is a tribal chief from South Waziristan. "The Americans might have supersonic jets and we might have to fight with stones in our hands, but we will stand up."
Analysts believe that U.S. intervention could set the tribal area on fire and reverse a series of recent setbacks for the militants. Some of the Pakistani tribes have risen up against the Taliban, in border areas of Dir and Bajaur, forming lashkars to fight them. The Pakistani military has finally taken on the extremists, in battles in Bajaur and Swat, a valley in the north west, while the democratic government has, for the first time, been trying to make the case to the public that the struggle against the militants is Pakistan's war, not America's.
However, allow me to repoint to the recent posting I made about an importan NYT magazine article: Why some U.S. troops called in air strikes on Pakistani border guards.