"The soldiers suspected that al-Qaida and Taliban members were travelling in the cars, in an attempt to flee to Afghanistan," Aljazeera's correspondent in Pakistan quoted official sources and eyewitnesses.
The dead were later proved to be citizens of the Angkor Eda area, he added.
Sensitivities are running high in the conservative region after Pakistan's army launched a raid on suspected fighters earlier this week.
In another incident armed men tried to sneak into a military compound in a remote tribal region where Pakistani forces have been hunting for members the Taliban and al-Qaeda, sparking a shootout, an army spokesman said on Saturday.
There were no casualties.
It was not immediately clear what motivated the raid, which happened at a big army compound in Wana near the Afghan border late on Friday - but Tribal leaders deeply resent the presence of the army in their lands.
Pakistani forces, however, have been slowly increasing their presence under pressure from Washington to crack down on al-Qaida and Taliban suspects.
Pakistan has stepped up efforts
to track down al-Qaida fighters
In an operation on Tuesday in Wana, troops arrested 25 suspected rebels.
Across the border in eastern Afghanistan, US troops also shot dead a fighter, the American military said.
The troops exchanged fire with several attackers on Wednesday near an American base at Orgun in Paktika province, 175km south of Kabul.
No American or allied Afghan soldiers were wounded, Lt Col Bryan Hilferty, a military spokesman, said on Saturday.
Hilferty provided few details of the incident and said the identity and affiliation of the attackers was unclear.
American and allied forces have been coming under regular fire in their bases and on patrol in Afghanistan.
Two rockets were fired overnight towards a US base in Khost, a province along the Pakistani border just north of Paktika, an Afghan official said.
The rockets missed their target and caused no injuries, said Hayat Allah Taniwal, a spokesman for the provincial governor.
Hilferty had no information on the reported attack.
So far this year, about 110 people have died in violence mainly in the south and east of the country, raising doubts about plans to hold national elections in June.