Another Pakistani security official said that US armoured vehicles were also seen moving on the Afghan side of the border, while US warplanes were seen overhead.
He also said that Pakistani soldiers had fired into the air, forcing the helicopters back across the border.
However, Major Murad Khan, a Pakistani military spokesman, said that although there had been shooting it did not involve Pakistani troops and the American helicopters had not crossed into Pakistani airspace.
"The US choppers were there at the border, but they did not violate our airspace," Khan said.
"We confirm that there was a firing incident at the time when the helicopters were there, but our forces were not involved."
Last week, General Ashfaq Kayani, the Pakistani army chief, said that Pakistan would not allow foreign troops on its soil and Pakistan's sovereignty and territorial integrity would be defended at all cost.
The New York Times newspaper reported last week that George Bush, the US president, had given clearance for US raids across the border.
South Waziristan, in the southern part of the country bordering Afghanistan, is seen by the US as a safe haven for supporters of the Taliban and al-Qaeda.