A confluence of five indicators escalates risk to Pakistan’s nuclear arsenal.  President Obama must help mitigate the brewing crisis before it becomes a horrific nightmare.

First, Pakistani Islamist groups have become the world’s most significant terrorist threat and capable of obtaining nuclear weapons, according to a new report by the Federation of American Scientists (FAS).  The Pakistani Neo-Taliban (PNT), the label given to the coalesced terrorist groups, has “conducted the most sophisticated, ambitious and operationally complex terrorist attacks in this century,” said Charles Blair, director of the Terrorism Analysis Project for FAS and author of the June 2011 report.

Blair states the PNT took root in Pakistan’s tribal areas after the Sept. 11, 2001, attacks.  “They [the Pakistanis] didn’t think that when the Taliban and al-Qaeda came into the tribal areas that they would target the Pakistani state,” Blair said.  But terrorist attacks inside Pakistan spiked at 1,916 incidents in 2009 and now Pakistan finds itself “in the midst of a civil war against many of these same forces.”

The PNT has become a “threat to the very existence of Pakistan” said U.S. Army Gen. David Petraeus in 2010, and according to Blair the PNT has a global agenda and is a “highly capable group that can seek and will seek nuclear weapons.”

Second, the physical security of Pakistan’s atomic arsenal warrants close examination, especially in light of America’s undetected airborne raid on Osama bin Laden’s lair in Abbottabad on May 2.  What does this security breach say about Pakistan’s nuclear insecurities, especially with regard to non-state actors such as the PNT?

The FAS report identified several PNT attacks conducted on or near Pakistani nuclear facilities.  The most recent incident was against Pakistan’s naval station Mehran on May 22.  Militants stormed the base with rocket launchers and hand grenades and killed 10 troops.  That well-fortified facility is 15 miles from Masroor Air Base, a depot for nuclear weapons.

But a senior U.S. State Department official believes Pakistan’s nuclear arsenal is safe from extremists, according to a report in the Indian Express.  “We don’t think there is any renewed concern … .  Those [nuclear] assets remain under much tighter security than what we saw in Pakistan’s naval base,” said Assistant Secretary of State Robert Blake.

Blake’s confidence is ill-placed.  The Baltimore-based Maldon Institute reported on nuclear thefts tracked by Shaun Gregory, the director of the Pakistan Security Research Unit at the University of Bradford in Britain.  Gregory’s report identifies attacks at a nuclear missile storage facility, a nuclear air base, and the nuclear weapons complex at the Wah Cantonment, Pakistan’s nuclear weapons assembly point.

Pakistani President Asif Ali Zardari and army chief Gen. Ashfaq Kayani insist their 100-odd atomic weapons are completely secure, and the U.S. has given Pakistan an estimated $100 million since 9/11 to harden its arsenal, train its people and improve surveillance.  But Gregory insists that despite “elaborate safeguards, empirical evidence points to a clear set of weaknesses and vulnerabilities in Pakistan’s nuclear safety and security arrangements.”

Third, one of those “vulnerabilities” is the cadre that oversees Pakistan’s atomic arsenal.  Pakistan’s military has traditionally been secular, but according to John McLaughlin, the former deputy director at the CIA, Pakistan’s security forces have become increasingly diverse.  There is evidence it is infiltrated at all levels by violent Islamists.

But Pakistani officials insist their nuclear personnel reliability program is stringent.  Retired Gen. Khaled Ahmed Kidwai, director general of the Strategic Plans Division, which oversees Pakistan’s nuclear weapons, told the New York Times, “Our security systems are foolproof.”

But how “foolproof” are Kidwai’s assurances if bin Laden, the world’s most wanted terrorist, can successfully “hide” in a Pakistani military town for five years without detection?  Obviously that incident humiliated Pakistan’s security forces and prompted some housecleaning.

Last month, Pakistani Brig. Gen. Ali Khan was taken into custody over accusations of ties with Hizb ut-Tahrir, a prohibited organization bent on achieving a worldwide Islamic theocracy (caliphate).  Then on June 22, Pakistani officials interrogated four army majors with alleged connections to Khan.  Are these actions for show, or has Pakistan really become serious about Islamists among its security forces?

Apparently, some security officials with Islamist sympathies have escaped the housecleaning.  In late May, Syed Saleem Shahzad, a Pakistani journalist who covered national security and terrorism, was found dead, his face horribly beaten, according to the New York Times.  He reportedly received repeated threats from the Inter-Services Intelligence (ISI), Pakistan’s chief intelligence agency.

Shahzad disappeared from Islamabad two days after he published an article suggesting the militant attack at naval station Mehran was retaliation for the navy’s attempt to crack down on al-Qaeda militants in the armed forces.

Fourth, Pakistan is expanding its atomic arsenal at a much faster rate than any other nation.  A soon-to-be-published study by the Bulletin of the Atomic Scientists, as reported by the Indian Press Online, states Pakistan could possess close to 200 atomic warheads within a decade that is more than Britain.

Chaudhry Ahmad Mukhtar, Pakistan’s minister of defense, tried to justify the larger atomic arsenal even as the domestic Islamist threat grows.  He explained India, Pakistan’s archenemy, was more financially capable of carrying on a prolonged war than Pakistan, according to the news agency Press Trust of India.  Therefore, one must surmise, Pakistan will make up the difference with atomic arms.

Finally, Pakistan has a history of nuclear proliferation.  “Those things that I fear in the future,” Adm. Michael Mullen, chairman of the U.S. Joint Chiefs of Staff, told the Associated Press, include “the proliferation of that [Pakistani nuclear weapon] technology, and it’s the opportunity and the potential that it could fall into the hands of terrorists.”

Pakistan acknowledges its scientists passed sensitive nuclear information to members of al-Qaeda, and in the 1970s A. Q. Khan, the father of Pakistan’s atomic bomb, covertly sold nuclear information and equipment to Libya, North Korea and Iran.  But it feigned ignorance of Khan’s proliferation activities until 2003, even though those transactions required extensive military logistical support.

These indicators of a brewing nuclear crisis coincide with a very strained U.S.-Pakistan relationship.  For example, Pakistan’s ambassador to the U.S., Husain Haqqani, told a May 2011 U.S. National Defense University audience that many Pakistanis consider America their “principal national security threat,” and, according to Dawn, a Pakistani newspaper, some Pakistani military officials believe the U.S. is determined to “denuclearize” their country.

President Obama must act quickly to mitigate Pakistan’s brewing nuclear crisis.  He should engage in a frank discussion with Pakistan’s senior leaders, offer positive inducements such as financial loans and aid, and security guarantees to leverage action to shore up nuclear surety.

But failing Pakistan’s immediate action, Obama must be prepared to curb aid and expand our operations against terrorist targets in Pakistan.  He must also be prepared to secure Pakistan’s atomic arsenal before it falls into the hands of Islamic jihadists with or without Islamabad’s cooperation, to prevent a hellish nuclear catastrophe in that country, the region and across the globe.