Helicopter gunships were then deployed to complete the operation. "I can't tell you the exact number of casualties, but most of them were killed," Sultan said.
While the army and a senior local official said the dead were fighters, and included some foreigners, a resident said the slain men were in fact Afghan labourers.
The south of Waziristan has long acted as a refuge for the Taliban and al-Qaeda, despite an army campaign that began in late 2003 to clear them out.
The army later struck a peace deal, but fighters linked to the Taliban grew in influence in the semi-autonomous tribal region, actively recruiting men and boys to fight in Afghanistan.
Last September, the government of General Pervez Musharraf struck another peace deal with tribal elders in neighbouring North Waziristan. Afghan, Nato and US forces in Afghanistan are concerned that this accord will also result in pro-Taliban and al-Qaeda elements gathering in strength.
Pakistan has been trying to find ways to isolate the fighters in Waziristan as it has lost of hundreds of troops in the fighting and wants to reduce the risk of inducing a wider conflict in the tribal areas.