One of the dead men was of Arab origin and the other was an Uzbek speaker, security officials said of Thursday's incident.
Paramilitary troops were hunting for the fourth man, who had escaped the fighting and fled to a nearby village, sources said.
Hundreds of people have been killed in clashes between fighters allegedly linked to al-Qaida and security forces over the past year in neighbouring South Waziristan.
Officials say about 100 foreign fighters, mainly from Central Asia, are still hiding in the rugged region, while hundreds more have either been killed or have fled to Afghanistan.
But they say they have found no sign of al-Qaida leader Usama bin Ladin or his deputy Ayman al-Zawahiri, who some experts say are somewhere in the Pakistan-Afghanistan border region.
Pakistan has arrested hundreds of suspected al-Qaida members and others since joining the "war on terror" declared by Washington after the 11 September 2001 attacks, many of whom have been handed over to the United States.