The move is to "penetrate, disrupt, defeat or destroy" al-Qa'ida and other groups in Iran, Saudi Arabia and Somalia, according to a secret directive signed in September by the top US commander in the Middle East, General David Petraeus.

US officials said the order also permitted reconnaissance that could pave the way for possible military strikes in Iran if tensions over its nuclear ambitions escalated, The New York Times reported.

The expansion in clandestine operations may strain US ties with allies in the region such as Washington-friendly governments in Saudi Arabia or Yemen, Pentagon officials warned.

The clandestine activities under the Joint Unconventional Warfare Task Force Execute Order, as the military directive is named, does not need as much oversight - such as White House approval for operations, and reporting to congress - as required with activities undertaken by the CIA.

While the Bush administration had approved some clandestine military activities far from designated war zones, the new order is intended to make such efforts more systematic and long-term, the paper said.