The CIA, using a mole inside al-Qaeda, identified the alleged mastermind as the terror group’s top operative on the Arabian peninsula, known as Swift Sword; but he was killed by Saudi security forces before the names of the terrorists, who had travelled to New York through North Africa, could be learnt.

The revelations are contained in The One Percent Doctrine by Ron Suskind, published in Time in the US and serialised by The Times.

The cyanide gas threat to the Subway was confirmed by the New York Police Department. “We were aware of the plot and took appropriate precaution,” a spokesman said.

The plan was discovered in early 2003 when a group of Bahraini jihadists, who had aroused the CIA’s suspicions, were arrested as they crossed from Saudi Arabia to the island kingdom, the book recounts.

Agents from a joint US- Saudi anti-terrorism unit found a laptop computer at a flat in Saudi Arabia that had been visited by one of them, described as “an educated fiftyish professional, with computer skills”. A copy of the hard-drive, sent for analysis to the United States, revealed the design of the mubtakkars to disperse hydrogen-cyanide gas in Subway carriages.

The design comprised two separate chambers for sodium cyanide, which is used as a rat poison and metal cleanser, and for a stable source of hydrogen, such as hydrochloric acid. A remote trigger could break a seal between the two, producing a lethal hydrogen-cyanide gas similar to the Zyklon B used in Nazi death camps.

“In the world of terrorist weaponry,” Suskind writes, “this was the equivalent of splitting the atom”.

The CIA immediatedly built a prototype, based on the captured design, that was about the size of a paint can and showed it the next morning to President Bush and Vice-President Dick Cheney. Mr Bush picked it up to feel its weight, Suskind reports. “Thing’s a nightmare,” he said.

US agents sought information about the plot from a mole inside al-Qaeda who had already been providing accurate tips for six months.

“There was a source from within Pakistan who was tied tightly into al-Qaeda management. Call him Ali,” Suskind writes. “Ali believed that bin Laden might have made a mistake in attacking America.”

“Ali” identified the key man in the plot as Osama bin Laden’s top operative on the Arabian peninsula, Yusuf al-Ayeri, known as Swift Sword.

The mole said that al-Ayeri had paid a visit in January 2003 to Zawahiri, bin Laden’s deputy, to inform him of the plot.

The cell members were just 45 days from launching the attack, he said, but Zawahiri called off the operation for unknown reasons that are still debated in the US intelligence community. Mr Bush voiced concern that Zawahiri did not want to disrupt plans for an even bigger attack.

In an interview with Time, Suskind said: “Al-Zawahiri called them off; he did not call them back. We have no reason to believe they’re not still here.”

Times Recommends

• No cause for celebration in crushed Sarajevo
• Jazz funeral for the final victims of Katrina
• French fined for 'insulting' civil servants