Well there was Nilore near Islamabad. In the 70's, it was practically bought by the Army and government and citizens were moved out after compensation. Research work got underway there. And it became a no go zone.
Now, it is a open city. But it still has a close attachment to nuclear program. PINSTECH and PIEAC are premier universities regarding nuclear research in Pakistan and are located there.
Nowadays, I don't know of any. Most of the program is now underground. It may seem like barren land of Balochistan, but under the sand and rock, there are huge complexes. Hospitals, officers messes, accommodation, offices, sites all are located underground now for those people dealing with this stuff directly.