Rafiuddin is said to be the right hand commander of Mehsud.
According to sources, another Taliban commander Zahir Shah was killed by the security forces in Tal area during a combing operation.
Huge cache of sophisticated arms and ammunition were seized in raids across the region, The Daily Times reports.
In an another incident, around 40 extremists attacked an army killing a security official and wounding several others.
"There were 30 to 40 Taliban who first fired rocket-propelled grenades at our post and then opened fire with AK-47 rifles which killed one of our soldiers. But we retaliated and killed six of them," a security official said.
Meanwhile, 35 suspected Taliban, including three important commanders were apprehended during search operations in Bara Tehsil of Khyber Agency.