KAMRA, PAKISTAN—A Heavily armed Taliban fighters blasted their way into a Pakistani air force base with possible links to the country’s nuclear program in a brazen assault that took two hours of fighting to put down, leaving a security officer and nine insurgents dead and underscoring the group’s continued threat despite numerous military offensives.

Hours later, Taliban gunmen in northern Pakistan forced 20 Shiite Muslims off buses, lined them up and killed them, the latest in a series of sectarian attacks that the government has seemingly done little to stop.

The separate incidents emphasize two daunting challenges the nuclear-armed country faces. The Pakistani Taliban continue to pose a potent threat despite numerous military offensives against their sanctuaries along the Afghan border. At the same time, sectarian violence plagues the Sunni majority country where Shiite Muslims often feel under attack.

While the Pakistani Taliban have carried out hundreds of bombings and other attacks, raids against military bases are somewhat uncommon. The group’s spokesman, Ahsanullah Ahsan, said they carried out Thursday’s pre-dawn attack as revenge for the death of Pakistani Taliban leader Baitullah Mehsud in a U.S. drone strike in 2009 and the American commando raid that killed Al Qaeda chief Osama bin Laden last year.

The large Air Force Base Minhas, located only about 40 kilometres northwest of Islamabad, hosts fighter jets, including F-16s, and contains a factory that makes aircraft and other weapons systems.

The weapons development and the presence of jets that could be used to deploy nuclear bombs have raised suspicions among some experts that the base is linked to Pakistan’s nuclear arsenal. However, no firm evidence has emerged, since the secrecy of the nuclear program makes independent evaluation difficult. The Pakistani military denies any connection between the base and the program.

The safety of the country’s nuclear weapons has been a major concern for the United States. Western experts say Pakistan has about 100 nuclear weapons and is expanding its arsenal.

“The great danger we’ve always feared is that if terrorism is not controlled in their country, that those nuclear weapons could fall into the wrong hands,” U.S. Defence Secretary Leon Panetta told Pentagon reporters Tuesday.

But many experts argue that the possibility of militants being able to battle their way inside a Pakistani facility and make out with a nuclear weapon or parts is extremely remote.

“There’s a lot of talk about the loose nukes and the security of the Pakistani nukes but this isn’t something that the Pakistani state is going to take lightly. This is one of their most prized possessions,” Kamran Bokhari, from the global intelligence firm, Stratfor.

In Washington, State Department spokeswoman Victoria Nuland told reporters the U.S. had no information that would contradict Pakistan’s denials that any nuclear material was at the Minhas base.

“As we’ve said all along, we have confidence that the government of Pakistan is well aware of the range of potential threats to its nuclear arsenal and has secured its nuclear arsenal accordingly,” she told reporters. “We don’t have any reason to be concerned at this moment.”

She said “Pakistanis have suffered more than their share at the hands of terrorists inside Pakistan, which speaks to our efforts to address this threat together and to try to address it as a community operating in that region.”

The Pakistani Taliban and its allies have waged a bloody insurgency against the government that has killed over 30,000 people. The military says its forces are stretched think battling the group — one reason, it says, it has not been able to do more against other militants in the country, particularly those attacking U.S. and NATO forces in neighbouring Afghanistan.

The Pakistani military has told the U.S. it plans to launch an offensive for the first time in North Waziristan, a militant stronghold on the border with Afghanistan. The campaign will aim to uproot the Pakistani Taliban but is expected to avoid tackling other militants involved in the Afghan war.

Thursday’s attack came at around 2 a.m., when Taliban militants opened a barrage of automatic weapons fire and rocket-propelled grenades at the base, according to the air force. Some of them were also wearing explosives strapped to their bodies, it said.

At least one of the rockets hit a hangar and damaged one of the aircraft parked inside, said air force spokesman Tariq Mahmood.

The attackers then scaled the wall surrounding the airbase and an intense firefight ensued.

After two hours, the security forces retook the base. By the end of the battle, one soldier and nine militants were killed, one of them when he blew himself up outside the base perimeter, the air force said. The commander in charge of the base was wounded in the shoulder.

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The Taliban have carried out several startling raids on military facilities in the past.

Half a dozen Taliban militants attacked a major naval base in the southern port city of Karachi in May 2011, killing at least 10 people and destroying two U.S.-supplied surveillance aircraft.

It took Pakistani commandos 18 hours to retake Naval Station Mehran, and two of the attackers escaped. That the attackers managed to infiltrate so deep into the high-security base led to speculation they may have had inside information or assistance.

In 2009, militants dressed in fatigues attacked army headquarters in the city of Rawalpindi, just outside Islamabad, and took 30 people hostage. Pakistani commandos finally raided the compound 22 hours later. Three captives and four militants were among those killed.

There have been at least three attacks in the vicinity of the Minhas base since 2007, but all of them occurred outside the installation.

In Thursday’s sectarian attack, gunmen forced 20 Shiites off three buses in the Naran Valley in northern Pakistan, shot and killed them, said a police official. He spoke on condition of anonymity because he was worried about retribution.

The victims were travelling from Rawalpindi to Gilgit, a mostly Shiite area, according to Gilgit’s deputy police inspector general, Ali Sher.

Later, two gunmen on a motorcycle shot and killed three Shiites in Quetta, the capital of Baluchistan province in southwest Pakistan, said police officer Shaukat Ali.

There have been several such sectarian attacks in the past by Sunni extremists who do not view Shiites as true Muslims. In February gunmen killed 16 Shiites in the city of Manshera. In April, violence between Sunnis and Shiites killed 14 people in and around Gilgit.

The attacks rarely elicit a strong response from the government of this Sunni-dominated country, and the military hardly ever launches military operations in response.

“The army has definitely not made it a cause that they have to defend the Shiites,” said Khalid Ahmed, a Pakistani scholar whose book “Sectarian War” investigates the country’s Sunni-Shiite divide.

The political parties rarely take up the cause because some of the Sunni groups have significant mainstream support, he said.

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