FATA is not under the provincial govt control. FATA (Federal Administered Tribal Area) is directly under the control of the Federal govt. However, Swat is a provincial administered area and that’s why the provincial govt with the help of the Pak Army cleaned up Swat from the gangsters.
If the Pak govt sincerely wants to clean up FATA, I am sure that can do it with no time and without any resistance.