WASHINGTON — The Central Intelligence Agency has used coercive interrogation methods against a select group of high-level leaders and operatives of Al Qaeda that have produced growing concerns inside the agency about abuses, according to current and former counterterrorism officials.
At least one agency employee has been disciplined for threatening a detainee with a gun during questioning, they said.
In the case of Khalid Shaikh Mohammed, a high-level detainee who is believed to have helped plan the attacks of Sept. 11, 2001, C.I.A. interrogators used graduated levels of force, including a technique known as "water boarding," in which a prisoner is strapped down, forcibly pushed under water and made to believe he might drown.
These techniques were authorized by a set of secret rules for the interrogation of high-level Qaeda prisoners, none known to be housed in Iraq, that were endorsed by the Justice Department and the C.I.A. The rules were among the first adopted by the Bush administration after the Sept. 11 attacks for handling detainees and may have helped establish a new understanding throughout the government that officials would have greater freedom to deal harshly with detainees.
Defenders of the operation said the methods stopped short of torture, did not violate American anti-torture statutes, and were necessary to fight a war against a nebulous enemy whose strength and intentions could only be gleaned by extracting information from often uncooperative detainees. Interrogators were trying to find out whether there might be another attack planned against the United States.
The methods employed by the C.I.A. are so severe that senior officials of the Federal Bureau of Investigation have directed its agents to stay out of many of the interviews of the high-level detainees, counterterrorism officials said. The F.B.I. officials have advised the bureau's director, Robert S. Mueller III, that the interrogation techniques, which would be prohibited in criminal cases, could compromise their agents in future criminal cases, the counterterrorism officials said.
After the attacks of Sept. 11, President Bush signed a series of directives authorizing the C.I.A. to conduct a covert war against Osama bin Laden's Qaeda network. The directives empowered the C.I.A. to kill or capture Qaeda leaders, but it is not clear whether the White House approved the specific rules for the interrogations.
The White House and the C.I.A. declined to comment on the matter.
The C.I.A. detention program for Qaeda leaders is the most secretive component of an extensive regime of detention and interrogation put into place by the United States government after the Sept. 11 attacks and the war in Afghanistan that includes the detention facilities run by the military in Iraq and Guantánamo Bay, Cuba.
There is now concern at the agency that the Congressional and criminal inquiries into abuses at Pentagon-run prisons and other detention centers in Iraq and Afghanistan may lead to examinations of the C.I.A's handling of the Qaeda detainees. That, in turn, could expose agency officers and operations to the same kind of public exposure as the military now faces because of the Iraq prison abuses.
So far, the agency has refused to grant any independent observer or human rights group access to the high-level detainees, who have been held in strict secrecy. Their whereabouts are such closely guarded secrets that one official said he had been told that Mr. Bush had informed the C.I.A. that he did not want to know where they were.
The authorized tactics are primarily those methods used in the training of American Special Operations soldiers to prepare them for the possibility of being captured and taken prisoners of war. The tactics simulate torture, but officials say they are supposed to stop short of serious injury.
Counterrorism officials say detainees have also been sent to third countries, where they are convinced that they might be executed, or tricked into believing they were being sent to such places. Some have been hooded, roughed up, soaked with water and deprived of food, light and medications.
Many authorities contend that torture and coercive treatment is as likely to provide information that is unreliable as information that is helpful.
Concerns are mounting among C.I.A. officers about the potential consequences of their actions. "Some people involved in this have been concerned for quite a while that eventually there would be a new president, or the mood in the country would change, and they would be held accountable," one intelligence source said. "Now that's happening faster than anybody expected."
The C.I.A.'s inspector general has begun an investigation into the deaths of three lower-level detainees held by the C.I.A in Iraq and Afghanistan. The Justice Department is also examining the deaths.
The secret detention system houses a group of 12 to 20 prisoners, government officials said, some under direct American control, others ostensibly under the supervision of foreign governments.
The C.I.A. high-level interrogation program seemed to show early results with the capture of Abu Zubaida in April 2002. Mr. Zubaida was a close associate of Mr. bin Laden's and had run Al Qaeda's recruiting, in which young men were brought from other countries to training camps in Afghanistan.
Under such intensive questioning, Mr. Zubaida provided useful information identifying Jose Padilla, a low-level Qaeda convert who was arrested in May 2002 in connection with an effort to build a dirty bomb. Mr. Zubaida also helped identify Mr. Mohammed as a crucial figure in the 9/11 plot, counterterrorism officials said.
A few other detainees have been identified by the Bush administration, like Ramzi bin al-Shibh, another 9/11 plotter and Walid Ba'Attash, who helped plan the East Africa embassy bombings in 1998 and the attack on the Navy destroyer Cole in October 2000.
Some of the prisoners have never been identified by the government. Some may have only peripheral ties to Al Qaeda. One Middle Eastern man, who had been identified by intelligence officials as a money launderer for Mr. bin Laden, was captured in the United Arab Emirates. He traveled there when some of the emirates' banks froze his accounts. When the U.A.E. government alerted the the C.I.A. that he was in the country, the man was arrested and subsequently disappeared into the secret detention program.
In the interrogation of Mr. Mohammed, C.I.A. officials became convinced that he was not being fully cooperative about his knowledge of the whereabouts of Mr. bin Laden. Mr. Mohammed was carrying a letter written by Mr. bin Laden to a family member when he was captured in Pakistan early in 2003. The C.I.A. officials then authorized even harsher techniques, according to officials familiar with the interrogation.
The C.I.A. has been operating its Qaeda detention system under a series of secret legal opinions by the agency's and Justice Department lawyers. Those rules have provided a legal basis for the use of harsh interrogation techniques, including the water-boarding tactic used against Mr. Mohammed.
One set of legal memorandums, the officials said, advises government officials that if they are contemplating procedures that may put them in violation of American statutes that prohibit torture, degrading treatment or the Geneva Conventions, they will not be responsible if it can be argued that the detainees are formally in the custody of another country.
The Geneva Conventions prohibit "violence to life and person, in particular . . . cruel treatment and torture" and "outrages upon personal dignity, in particular, humiliating and degrading treatment."
Regarding American anti-torture laws, one administration figure involved in discussions about the memorandums said: "The criminal statutes only apply to American officials. The question is how involved are the American officials."
The official said the legal opinions say restrictions on procedures would not apply if the detainee could be deemed to be in the custody of a different country, even though American officials were getting the benefit of the interrogation. "It would be the responsibility of the other country," the official said. "It depends on the level of involvement."
Like the more numerous detainees at Guantánamo Bay, the high-level Qaeda prisoners have also been defined as unlawful combatants, not as prisoners of war. Those prisoners have no standing in American civilian or military courts.
The Bush administration began the program when intelligence agencies realized that a few detainees captured in Afghanistan had such a high intelligence value that they should be separated from the lower-level figures who had been sent to a military installation at Guantánamo Bay, which officials felt was not suitable.
There was little long-term planning. The agency initially had few interrogators and no facilities to house the top detainees. After the Sept. 11 attacks, the agency began to search for remote sites in friendly countries around the world where Qaeda operatives could be kept quietly and securely.
"There was a debate after 9/11 about how to make people disappear," a former intelligence official said.
The result was a series of secret agreements allowing the C.I.A. to use sites overseas without outside scrutiny.
So far, the Bush administration has not said what it intends to do over the long term with any of the high-level detainees, leaving them subject to being imprisoned indefinitely without any access to lawyers, courts or any form of due process.
Some officials have suggested that some of the high-level detainees may be tried in military tribunals or officially turned over to other countries, but counterterrorism officials have complained about the Bush administration's failure to have an "endgame" for these detainees. One official said they could also be imprisoned indefinitely at a new long-term prison being built at Guantánamo.
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