Pakistans current nuclear security situation is uncertain. While the weapons are in secure storage areas for the present, their safety in a scenario in which Musharrafs government crumbled would be at risk (Mufson). Even assuming Musharraf retains power, the potential for theft of one of their weapons is not far-fetched. A significant portion of the nuclear scientists employed in Pakistans nuclear program is believed to be Islamic fundamentalists who had maintained strong ties with the Taliban government (Mufson). This could potentially lead to a weapon either being hijacked using insider information or smuggled out of the country to a terrorist network. Other fears include a rogue commander ordering their use during a confrontation with India, independent groups storming one of the military sites where the weapons are stored, or a military mutiny (Bidwai).

Pakistans military is rumored to be splintered among a variety of factions, some of which are sympathetic to extremist Muslim groups (Kampani). While specific knowledge about whether or not Pakistan has PALS is unclear (at times Pakistani officials have given conflicting statements about this specific issue), it is generally believed that the weapons probably have no password systems and at best possess very primitive ones (Bidwai).

The most recent comments from Pakistani officials on the matter come from General Kidwai, who told visiting scholars from an Italian research institute that Pakistan does not possess any PALS or similar encoding systems (Cotta-Ramusino and Martellini). This same delegation found that the only significant security restriction to prevent unauthorized nuclear use was a 3-men rule that required the concurrent agreement of 3 people on the decision to use the weapon.