The Kuwaiti man, who was captured in Indonesia in 2002 and turned over to the United States, was among four prisoners who fled heavily fortified Bagram Air Base prison on 10 July, the officials said on Wednesday. He remains at large.
The officials, who asked not to be identified, did not explain why the United States did not reveal al-Faruq was among the four men until pressed by lawyers this week at a military trial in Texas of an Army sergeant charged with maltreating detainees in Afghanistan.
At the time of his capture in June 2002, al-Faruq was al-Qaida's most senior operative in Southeast Asia, according to intelligence officials.
"Al-Faruq was one of the four who escaped on July 10 from the Bagram detention facility," said one of the defense officials at the Pentagon.
Security stepped up
In Kabul, the US military released a statement saying that prison security procedures were bolstered after the breakout of the four men and that a search for them continued with help from Afghanistan's government.
Faruq's disappearance did not come to light until defense attorneys for Army Sergeant Alan Driver demanded on Tuesday to know where the al-Qaida operative was so he could testify at the military trial. Military prosecutors conceded they could not produce him as a witness because he had escaped.
Osama bin Laden reportedly sent
Omar al-Faruq to Southeast Asia
Al-Faruq was sent to Southeast Asia in 1998 by al-Qaida leader Osama bin Laden to expand the network's operations in the region. He linked up with Jemaah Islamiah, a militant group dedicated to creating a Muslim empire in Southeast Asia, and has been implicated in several bomb attacks in Indonesia.
After being taken to the US jail at Bagram and subjected to three months of interrogation techniques that included sleep deprivation and isolation, al-Faruq told investigators several US embassies in Southeast Asia would be attacked on 11 September 2002.
The information prompted the closure of several embassies and the raising of the US security alert level to orange - the second-highest - but the attacks did not occur.
Al-Faruq also implicated Indonesian cleric Abu Bakar Bashir, who intelligence officials say is the spiritual leader of Jemaah Islamiah, in planning bomb attacks in the region. Bashir denies involvement in terrorism.
The escape in Afghanistan was the first known one from the heavily guarded detention centre deep within the sprawling Bagram Air Base, 50km north of the capital, Kabul.