Pakistan's nuclear facilities have been attacked three times by home-grown extremists over the past two years, a senior U.S. official has confirmed to FOX News.

Three separate facilities in Pakistan — each of which deals in some part with nuclear activity — have been targeted by extremists, the official said, while insisting that there is "no waning confidence regarding the safety of the Pakistani nuclear program."

The official confirmed a report in West Point's Combating Terrorism Center Sentinel describing an attack on a nuclear missile storage facility at Sargodha on Nov. 1, 2007, and a homicide bombing at the nuclear airbase at Kamra on Dec. 10, 2007.

The report also notes a much larger raid by the Pakistani Taliban on Aug. 20, 2008, when homicide bombers blew up several entry points to an armament complex at the country's main nuclear facility, the Wah Cantonment Ordnance Complex.

A Pakistani official told FOX News the report was "out of context" but stopped well short of saying the attacks did not occur.

"Pakistan's nuclear facilities are safe — there is no likelihood of terrorist activity at those sites," the official told FOX News. "This report is out of context. The incidents that are mentioned here have no link to our facilities."

The U.S. official said it's not clear whether the attackers knew what they were targeting — and added that they would need to do much more to take control of Pakistan's nuclear arsenal.

"Touching off an explosive from the gate checkpoint doesn't get you in," the official told FOX News. The Wah complex is a huge facility that does more than just nuclear work, the official said.

"We are of the view these incidents did occur but we are not sure you can extrapolate a downgrade of security surrounding the Pakistani nuclear arsenal."

But resurgent jihadists in Pakistan still have the U.S. worried over the safety of the country's nuclear weapons.

The U.S. has a detailed plan for infiltrating Pakistan and securing its mobile arsenal of nuclear warheads if it appears the country is about to fall under the control of the Taliban, Al Qaeda or other Islamic extremists, as FOXNews.com reported in May.

"The challenge to Pakistan's nuclear weapons from Pakistani Taliban groups and from al-Qa'ida constitutes a real and present danger," writes security expert Shaun Gregory in the West Point report.

Homegrown attacks in that shaky democracy have occurred even as Pakistan has taken steps to safeguard its stockpile against potential strikes, writes Gregory, the director of the Pakistan Security Research Unit at the University of Bradford in the U.K.

Gregory's paper, "The Terrorist Threat to Pakistan's Nuclear Weapons," notes that Pakistan's nuclear infrastructure was developed to ward off external attacks from India — not internal strikes from groups like the Taliban.

FOX News' Justin Fishel and Nina Donaghy contributed to this report.