instead of the Navy. however the Army has its own say as well, because its the one that provides security. Supposedly about 2 Divisions are used to guard the Pakistani Nukes, probably spread out all over the country. However its almost a given that they will tend to be near Pakistani Air-force base as the F16's are the only aircraft pakistan has which can carry nukes...the rest will be in ballistic missile warheads.
The Sargodha PAF airbase is supposedly the biggest such base associated with nukes.
here is a google map pic of that base with the hardened shelters numbered
here is another pic of that region showing recent tunnel dug into a nearby mountain using Chinese help. It will be not too hard to guess what will be stored inside.
Some of the suspected nuclear storage sites are
Sargodha PAF AFB
Minwali PAF AFB
Masroor PAF AFB
Samungli PAF AFB
Kohat PAF AFB
Rafiqui PAF AFB
Chaklala PAF AFB
Peshawar PAF AFB
Kamra PAF AFB
According to US officials, there seems to be some plan in place for American forces to take-over(??? would be pretty dangerous) the Pakistani nuclear facilities in the event of a coup/Fundie takeover. The window of opportunity for such an operation will be extremely limited..given that the fundies might be more than willing to launch the nukes the moment tget get control...even if it means they will die as well(kinda hard to reason with a person who is looking to get into "heaven" by killing kafirs). Not only will the American forces have to take over these highly guarded installations by fighting the security there..but they have to do it before any nukes are launched. In the event of a launch all these sites will be immediately turned into parking lots by retaliatory strikes..and if American forces are in the vicinity they will be caught in the middle.
This is what makes the entire situation really dangerous because if Pakistan collapses India, America and surrounding nations will be in HUGE trouble.Thus the unfortunate situation of being forced to walk a tightrope while dealing with Pakistan. Its a country too dangerous to fail. :(. For the sake of millions of people I really hope the Pakistanis are able to guard their nukes, but my biggest fear is that there are fundamentalist moles in the forces guarding the nukes...its almost a given...a point reinforced when allegations about inside job/support surfacing about today's attack in the naval base.