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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.”