Now they tell us. From the New York Times, Nov. 10, links and emphasis added:

Secret Order Lets U.S. Raid Al Qaeda
WASHINGTON — The United States military since 2004 has used broad, secret authority to carry out nearly a dozen previously undisclosed attacks against Al Qaeda and other militants in Syria, Pakistan and elsewhere, according to senior American officials.

These military raids, typically carried out by Special Operations forces, were authorized by a classified order that Defense Secretary Donald H. Rumsfeld signed in the spring of 2004 with the approval of President Bush, the officials said. The secret order gave the military new authority to attack the Qaeda terrorist network anywhere in the world, and a more sweeping mandate to conduct operations in countries not at war with the United States.

In 2006, for example, a Navy Seal team raided a suspected militants' compound in the Bajaur region of Pakistan, according to a former top official of the Central Intelligence Agency. Officials watched the entire mission — captured by the video camera of a remotely piloted Predator aircraft — in real time in the C.I.A.'s Counterterrorist Center at the agency's headquarters in Virginia 7,000 miles away.

Some of the military missions have been conducted in close coordination with the C.I.A., according to senior American officials, who said that in others, like the Special Operations raid in Syria on Oct. 26 of this year, the military commandos acted in support of C.I.A.-directed operations.

[...]

More than a half-dozen officials, including current and former military and intelligence officials as well as senior Bush administration policy makers, described details of the 2004 military order on the condition of anonymity because of its politically delicate nature. Spokesmen for the White House, the Defense Department and the military declined to comment.

Apart from the 2006 raid into Pakistan, the American officials refused to describe in detail what they said had been nearly a dozen previously undisclosed attacks, except to say they had been carried out in Syria, Pakistan and other countries. They made clear that there had been no raids into Iran using that authority, but they suggested that American forces had carried out reconnaissance missions in Iran using other classified directives.

According to a senior administration official, the new authority was spelled out in a classified document called "Al Qaeda Network Exord," or execute order, that streamlined the approval process for the military to act outside officially declared war zones. Where in the past the Pentagon needed to get approval for missions on a case-by-case basis, which could take days when there were only hours to act, the new order specified a way for Pentagon planners to get the green light for a mission far more quickly, the official said.

[...]

The 2004 order identifies 15 to 20 countries, including Syria, Pakistan, Yemen, Saudi Arabia and several other Persian Gulf states, where Qaeda militants were believed to be operating or to have sought sanctuary, a senior administration official said.

Even with the order, each specific mission requires high-level government approval. Targets in Somalia, for instance, need at least the approval of the defense secretary, the administration official said, while targets in a handful of countries, including Pakistan and Syria, require presidential approval.

The Pentagon has exercised its authority frequently, dispatching commandos to countries including Pakistan and Somalia. Details of a few of these strikes have previously been reported.

For example, shortly after Ethiopian troops crossed into Somalia in late 2006 to dislodge an Islamist regime in Mogadishu, the Pentagon's Joint Special Operations Command quietly sent operatives and AC-130 gunships to an airstrip near the Ethiopian town of Dire Dawa. From there, members of a classified unit called Task Force 88 crossed repeatedly into Somalia to hunt senior members of a Qaeda cell believed to be responsible for the 1998 American Embassy bombings in Kenya and Tanzania.

At the time, American officials said Special Operations troops were operating under a classified directive authorizing the military to kill or capture Qaeda operatives if failure to act quickly would mean the United States had lost a "fleeting opportunity" to neutralize the enemy.

Occasionally, the officials said, Special Operations troops would land in Somalia to assess the strikes' results. On Jan. 7, 2007, an AC-130 struck an isolated fishing village near the Kenyan border, and within hours, American commandos and Ethiopian troops were examining the rubble to determine whether any Qaeda operatives had been killed.

But even with the new authority, proposed Pentagon missions were sometimes scrubbed because of bad intelligence or bureaucratic entanglements, senior administration officials said.

The details of one of those aborted operations, in early 2005, were reported by The New York Times last June. In that case, an operation to send a team of the Navy Seals and the Army Rangers into Pakistan to capture Ayman al-Zawahri, Osama bin Laden’s top deputy, was aborted at the last minute.

Mr. Zawahri was believed by intelligence officials to be attending a meeting in Bajaur, in Pakistan's tribal areas, and the Pentagon's Joint Special Operations Command hastily put together a plan to capture him. There were strong disagreements inside the Pentagon and the C.I.A. about the quality of the intelligence, however, and some in the military expressed concern that the mission was unnecessarily risky.

Porter J. Goss, the C.I.A. director at the time, urged the military to carry out the mission, and some in the C.I.A. even wanted to execute it without informing Ryan C. Crocker, then the American ambassador to Pakistan. Mr. Rumsfeld ultimately refused to authorize the mission.

Former military and intelligence officials said that Lt. Gen. Stanley A. McChrystal, who recently completed his tour as head of the Joint Special Operations Command, had pressed for years to win approval for commando missions into Pakistan. But the missions were frequently rejected because officials in Washington determined that the risks to American troops and the alliance with Pakistan were too great.

Capt. John Kirby, a spokesman for General McChrystal, who is now director of the military's Joint Staff, declined to comment.

The recent raid into Syria was not the first time that Special Operations forces had operated in that country, according to a senior military official and an outside adviser to the Pentagon.

Since the Iraq war began, the official and the outside adviser said, Special Operations forces have several times made cross-border raids aimed at militants and infrastructure aiding the flow of foreign fighters into Iraq.

The raid in late October, however, was much more noticeable than the previous raids, military officials said, which helps explain why it drew a sharp protest from the Syrian government.

Negotiations to hammer out the 2004 order took place over nearly a year and involved wrangling between the Pentagon and the C.I.A. and the State Department about the military's proper role around the world, several administration officials said.

American officials said there had been debate over whether to include Iran in the 2004 order, but ultimately Iran was set aside, possibly to be dealt with under a separate authorization.

[...]

The 2004 order also provided a foundation for the orders that Mr. Bush approved in July allowing the military to conduct raids into the Pakistani tribal areas, including the Sept. 3 operation by Special Operations forces that killed about 20 militants, American officials said.

Administration officials said that Mr. Bush's approval had paved the way for Defense Secretary Robert M. Gates to sign an order — separate from the 2004 order — that specifically directed the military to plan a series of operations, in cooperation with the C.I.A., on the Qaeda network and other militant groups linked to it in Pakistan.

Unlike the 2004 order, in which Special Operations commanders nominated targets for approval by senior government officials, the order in July was more of a top-down approach, directing the military to work with the C.I.A. to find targets in the tribal areas, administration officials said. They said each target still needed to be approved by the group of Mr. Bush's top national security and foreign policy advisers, called the Principals Committee.

See our last posts on al-Qaeda and politics of the GWOT.