"There were about 37 paramilitary troops in the fort and seven of them were able to escape while the rest of them are missing and feared dead," the official, who declined to be identified, said.
Security forces have been battling al-Qaeda-linked fighters in South Waziristan for several years.
The Sara Rogha area is a stronghold of Baitullah Mehsud, an al-Qaeda-linked leader who the Pakistani government say was behind the assassination of Benazir Bhutto, former primer minister and opposition leader, on December 27.
Security forces were firing artillery in the area on Wednesday morning but it was not immediately clear what their target was, residents said.
Another security official said six tribal fighters had been killed during fighting overnight.
Separately, a roadside bomb exploded as a military patrol was passing along the Swat valley in North West Frontier Province on Wednesday but there was no immediate word on casualties, police said.