Issued last September by General David Petraeus, the order authorized an escalation that included boosting military and intelligence assistance to help Yemeni forces strike al Qaeda targets, as well as deployment of more unmanned aerial drones to collect information and track high-value targets.
The order also authorized U.S. Special Operations units to work with local security forces to counter al Qaeda and other threats, a goal Pentagon officials have made no secret of.
As the head of the U.S. military's Central Command, Petraeus oversees U.S. wars in Iraq and Afghanistan and plays a major role in planning for any possible military action against Iran over its nuclear program.
The order was first reported by the New York Times, which quoted a document it obtained as saying the goal was to build networks that could "penetrate, disrupt, defeat or destroy" al Qaeda and other militant groups as well as "prepare the environment" for future attacks by U.S. or local military forces.
The newspaper said the directive also appeared to authorize specific operations in Iran, most likely to gather intelligence about its nuclear program or identify dissident groups that might be useful for any future military offensive.
Some of the covert military operations that followed the secret order have been reported. These include a September 2009 attack by helicopter-borne Special Operations Forces on a car carrying one of east Africa's most wanted al Qaeda militants, Kenyan-born Saleh Ali Saleh Nabhan.
Central Command has been positioning Reaper drones at a base in the Horn of Africa. Officials said the drones can be used against militants in Yemen and Somalia, and even against pirates who attack ships traversing the Gulf of Aden and the Indian Ocean.
"They (the drones) are part of it but it is much broader than that," one U.S. official said of the order.
In February, Defense Secretary Robert Gates authorized $150 million in security assistance for Yemen for fiscal 2010, up from $67 million last year.
Officials told Reuters the money would be used in part to bolster Yemen's special operations forces to lead an offensive targeting al Qaeda in the Arabian Peninsula, which claimed responsibility for a failed plot to blow up a U.S. passenger plane on Christmas Day.
The group has emerged as one of al Qaeda's most active affiliates, and the Obama administration recently took the extraordinary step of authorizing the CIA to kill a leading figure linked to the group -- American-born Muslim cleric Anwar al-Awlaki.
(Reporting by Adam Entous; Editing by Chris Wilson)