The Justice Department on Thursday closed a second review into whether CIA interrogators mistreated detainees and recommended a criminal probe of the deaths of two captives under CIA custody.
The news was conveyed to CIA employees in a note from Leon E. Panetta on his last day as the agency's director.
"On this day, my last day as director, I welcome news that the broader inquiries are behind us," he said. "We are now finally about to close this chapter of our agency's history."
Meanwhile, the Senate voted to confirm Mr. Panetta's replacement at the agency, former Afghanistan commander Gen. David H. Petraeus, by a vote of 94-0.
The Justice Department investigation, led by Assistant U.S. Attorney John Durham, was reopened into suspected detainee abuse. It was closed in 2008, the last full year of the Bush administration.
Attorney General Eric H. Holder Jr. appointed Mr. Durham in August 2009 to look into the treatment of prisoners at so-called "black sites" overseas.
On Thursday, Mr. Holder announced that the department is declining to investigate the rest of the more than 100 cases that have been under review by Mr. Durham for almost two years.
"Mr. Durham has advised me of the results of his investigation, and I have accepted his recommendation to conduct a full criminal investigation regarding the death in custody of two individuals," Mr. Holder said in a statement. "Those investigations are ongoing. The department has determined that an expanded criminal investigation of the remaining matters is not warranted."
Mr. Holder said Mr. Durham's review "included both information and matters that had never previously been examined by the department."
The Justice Department has not provided any details about the two incidents, which it will continue to investigate.
The CIA came under scrutiny in 2005 amid allegations that a detainee died of hypothermia in an abandoned warehouse used as a CIA facility outside of Kabul, Afghanistan, known as "the salt pit."
Mr. Durham's inquiry examined 101 reputed instances of CIA abuse of detainees. After Sept. 11, 2001, the Justice Department's office of legal counsel approved harsher interrogation techniques, such as simulated drowning for suspected terrorists captured in the war against al Qaeda.
Mr. Durham examined whether CIA officers employed harsher techniques that were not approved by the Justice Department.
The CIA also set up secret prisons in Europe and other parts of the world, where these detainees were interrogated.
Mr. Durham's new investigation was of particular concern to the agency because of fears that it would place officers in double jeopardy. Some CIA officers have taken out special insurance policies to protect themselves and their families from civil and criminal prosecutions.
Seven former CIA directors in 2009 wrote a letter to President Obama urging him to abandon Mr. Durham's inquiry.
"If criminal investigations closed by career prosecutors during one administration can so easily be reopened at the direction of political appointees in the next, declinations of prosecution will be rendered meaningless," the directors wrote.
In 2008, Attorney General Michael B. Mukasey appointed Mr. Durham to investigate the destruction of dozens of CIA videotapes of detainee interrogations.
In 2005, the CIA destroyed video recordings of the waterboarding of Abu Zubaydah, accused in the plot of the Sept. 11, 2001, attacks. Former CIA Director Gen. Michael V. Hayden has said public disclosure of the tapes could have placed CIA officers who conducted the interrogations at risk of reprisals from al Qaeda.
While the CIA opposed the investigations, civil liberties groups held out hope the Justice Department's investigation would end in the prosecutions of senior Bush administration officials.
When Mr. Holder announced Mr. Durham's review on Aug. 24, 2009, Anthony Romero, executive director of the American Civil Liberties Union, said, "Holder's decision not to launch a full investigation is deeply troubling, given the evidence already in the public domain, of crimes that were committed. Any investigation that truly follows the facts where they lead would inevitably lead to prosecutions of high-level officials, not just rogue agents in the field."
On Thursday, Jameel Jaffer, deputy legal director at the ACLU, welcomed the Justice Department announcement of criminal investigations of the two detainee deaths. But, he said, "it is difficult to understand the prosecutor's conclusion that only those two deaths warrant further investigation."
"For a period of several years, and with the approval of the [George W.] Bush administration's most senior officials, the CIA operated an interrogation program that subjected prisoners to unimaginable cruelty and violated both international and domestic law," he said. "The narrow investigation that Attorney General Holder announced today is not proportionate to the scale and scope of the wrongdoing."
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