The attack took place in the Kalundar Keley area of South Waziristan, about 60 kilometres (37 miles) north of the district's main town Wana.
"Militants attacked a security force patrol on Tuesday in Kalundar Keley area, killing three troops and wounding two others," a senior security official in the area told AFP on condition of anonymity.
The official said an earlier roadside bomb attack in the same area wounded two more soldiers. A second security official confirmed the deaths.
Pakistan carried out a major ground and air offensive in South Waziristan last year that was designed to evict the Tehreek-e-Taliban faction, which has been blamed for some of the country's worst violence, from its headquarters.
Many of its commanders and footsoldiers are believed to have fled into neighbouring North Waziristan, considered the ultimate fortress of Al-Qaeda and Taliban affiliates in Pakistan's semi-autonomous tribal belt.
Pakistani officials have been angered by reports of mounting US pressure on the military to launch an offensive against militants fighting against American troops in Afghanistan but who are based in North Waziristan.
The United States and Pakistan will on Wednesday open a "strategic dialogue," an initiative launched by the United States earlier this year to show that it cares about more than just Pakistan's help in Afghanistan.
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