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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.
Senior officials of the State Department and the C.I.A. voiced fears that military commandos would encroach on their turf, conducting operations that historically the C.I.A. had carried out, and running missions without an ambassador’s knowledge or approval.
Mr. Rumsfeld had pushed in the years after the Sept. 11 attacks to expand the mission of Special Operations troops to include intelligence gathering and counterterrorism operations in countries where American commandos had not operated before.
Bush administration officials have shown a determination to operate under an expansive definition of self-defense that provides a legal rationale for strikes on militant targets in sovereign nations without those countries’ consent.
Several officials said the negotiations over the 2004 order resulted in closer coordination among the Pentagon, the State Department and the C.I.A., and set a very high standard for the quality of intelligence necessary to gain approval for an attack.
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.
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