The New York Times revealed on its website late Sunday that US forces had carried out 'reconnaissance missions in Iran' and conducted about a dozen secret attacks in about 20 countries.
According to the officials who disclosed the issue, no military mission has been carried out in Iran.
US Special Operations forces carried out the military raids in line with a classified order signed by then-defense secretary Donald Rumsfeld in the spring of 2004 with the approval of President George W. Bush, the daily reported unnamed top US officials as saying.
The officials claim the order authorized the operations against various groups Washington considers as terrorists.
Some of the operations, such as the recent US cross-border attack on Syria on October 26, have reportedly been conducted in close cooperation with the Central Intelligence Agency (CIA).
In a letter to the United Nations, Syria condemned the US attack on its border village. The raid killed eight people, four of whom were children.
The Times also quoted a former top CIA official as saying that in another operation a Navy Seal team raided a suspected militant compound in the Bajaur region of Pakistan in 2006.
Pakistan, a US 'war on terror' ally, has been a target of numerous US drone attacks in recent months. Washington has reportedly carried out more than 45 strikes and intrusions into the country in the past seven months.
Islamabad has repeatedly condemned the air raids and has urged Washington to stop all such operations, saying that the incursions have been 'violating the country's sovereignty'.
According to the paper, the Pentagon required approval for each and every mission carried out before the 2004 order. Rumsfeld and Bush, however, demanded automatic use of military power.
The 2004 order identifies 15 to 20 countries, including Syria, Pakistan, Yemen, Saudi Arabia and several other Persian Gulf littoral states.
The report comes as investigative journalist Seymour Hersh revealed in July that US congressional leaders secretly agreed last year to President Bush's $400-million funding request for a major escalation in covert operations in Iran.