Pakistan's foreign ministry blasted the article as "utterly misleading and totally baseless", calling it "nothing more than a concoction to tarnish the image of Pakistan and create misgivings among its people".
The ministry also accused Hersh of making "several false and highly irresponsible claims by quoting anonymous and unverifiable sources".
"Pakistan's strategic assets are completely safe and secure ... Pakistan, as a sovereign state, will never allow any country to have direct or indirect access to its nuclear and strategic facilties. Any suggestion to this effect is simply preposterous".
In his article, Hersh alleged that the US has a covert team ready to fly into Pakistan at a moment's notice and defend nuclear installations from attack.
'Emergency response team'
Hersh also said he has evidence the US administration has been working on "highly sensitive understandings" with Pakistan's military that would let the US military provide "added security for the Pakistani arsenal in case of a crisis".
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"The United States has no intention to seize Pakistani nuclear weapons or materials."
Larry Schwartz,
US embassy spokesman in Pakistan
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The Pakistani military, for example, would be given money to equip and train Pakistani soldiers and to improve their housing and facilities, Hersh said.
Hersh also claimed that a "highly classified" emergency response team had already been activated within the past few months in response to a report that a Pakistani nuclear component had "gone astray".
It is not the first time Hersh has made such a claim. In November 2001, another of his articles on Pakistan's nuclear programme stirred a similar controversy.
Hersh reported at that time that Washington was making plans to seize or disable Pakistani nuclear weapons to prevent them from falling into the hands of Islamic fighters.
That report was met with widespread denials as well.
Larry Schwartz, a US embassy spokesman in Pakistan, did not confirm or deny the latest report but noted Hillary Clinton, the US secretary of state, had full confidence in Islamabad's ability to protect its own nuclear programmes and materials.
"The United States has no intention to seize Pakistani nuclear weapons or material," Schwartz said. "Pakistan is a key ally in our common effort to fight violent extremists and foster regional security. We work co-operatively with Pakistan on a wide range of security assistance initiatives."
Estimates of Pakistan's nuclear arsenal currently range from 60 to 100 weapons. It first declared its status as a nuclear power in 1998, testing five bombs in a tit-for-tat with its south Asian neighbour, India.