"We do provide them with assistance, as you know," he said, but added: "We have confidence in the ability of the Pakistani government to provide adequate security for their nuclear programmes and materials."
Rapid response force
Hersh, a Pulitzer prize-winning writer, said in his report that the US and Pakistan have agreed on a security protocol allowing a special US team to assist in the guarding of Pakistan's nuclear armaments.
"There certainly is a rapid response force; I'll take it a step further – it is called a 'Tailored Fest'," he told Al Jazeera on Tuesday.
"I just wish they would not deny stuff that is actually publicly available if you know where to look for it. It is a force that [will act] in case of any nuclear incident or any other terrorism-related incident.
"The men, and the women, who I assume will work on it include not only US state department counter-terror people but also the CIA, the FBI and other special operators, as a unified team.
"They have to report within four hours of a crisis to Andrews air field [in Washington DC] and be sent on their way."
Hersh said that the unit was scrambled last summer to respond to an alert in Pakistan, but the incident proved to be a false alarm.
"There was a report that turned out to be aborted [about] some nuclear incident, probably a missing nuke in Pakistan. This is a super worry for the United States of America, and it always has been," Hersh said.
Pakistan is thought to have set up its nuclear programme in 1971, soon after a war with India. The country is estimated to possess between 60 and 120 nuclear weapons.
The Pentagon has said the US is providing some training and equipment to Pakistan to improve its nuclear security.
Hillary Clinton, the US secretary of state, said in the wake of an attack on Pakistan's military headquarters in Rawalpindi in October that Washington had "confidence in the Pakistani government's control over nuclear weapons".
|Pakistan is believed to have between 60 and 120 nuclear weapons [EPA]
But during a subsequent visit to Pakistan, she urged Islamabad to acknowledge the threat of what she called "nuclear-armed extremists", while calling on the country to join nuclear non-proliferation talks.
Washington and Islamabad have each denied that US special forces are on standby inside Pakistan, but Hersh insists they are there.
"Eight years ago I wrote about another group in the New Yorker, right after 9/11. [That group] had been set up in the late 90s in the Pentagon.
"So there are at least two groups that are involved, and there is probably a separate group in the [US] department of energy that also does stuff," Hersh told Al Jazeera.
"So we have a lot of groups that have a lot of responsibility in case of a nuclear crisis. The group I am writing about [now], which is on a standby basis, I think is basically in [Pakistan], whether it is in Islamabad or the US embassy.
"This is a standby group whose mission is in case of trauma inside Pakistan – we are not talking about the Pakistani Taliban taking over, that is not going to happen – but basically in case of a mutiny … they are there in case the Pakistanis want back-up."