Security officials said the attack was launched during the early afternoon on Monday on the slopes of a mountain called Khawaja Khizer.
The three were brought to the Pakistani border town of Angoor Adda from a nearby mountain where they had been mining for minerals, but another eight men were unaccounted for, said the officials, who requested anonymity.
A senior Pakistani military official, also speaking on condition of anonymity because he was unauthorised to speak to the media, said two missiles landed close to the South Waziristan town of Angoor Adda near a quarry on Khawaja Khizer mountain.
The official said Pakistan was investigating whether US forces were involved and will lodge a protest if a fact-finding team sent to the area uncovers information indicating American involvement.
Angoor Aada is about 300m from the Afghan border.
Initially, officials had said helicopter gunships had carried out the attack, but others later said it had been aircraft.
A US military spokesman in Afghanistan said American helicopters launched an air strike on a truck carrying munitions near the Afghan side of its border with Pakistan, but denied any missiles landing in Pakistan.
Lieutenant Colonel Paul Fitzpatrick said: "We struck it [the truck] and then we went to the ground and went to a cave and found two more ... trucks loaded with rockets.
"This was a large weapons storage cache hidden in a cave and this was in Afghanistan."
Fitzpatrick said the attack happened near the border opposite Pakistan's volatile North Waziristan tribal region.
About 2,500 American and Afghan soldiers have been hunting Taliban and al-Qaeda-linked fighters in eastern Afghanistan for the past month in a large-scale operation.