The Justice Department will not file criminal charges over the destruction of CIA videotapes depicting the harsh interrogation of terrorism suspects, limiting the legal fallout from one of the Bush administration's most fraught legacies, officials said Tuesday.

After an exhaustive probe that lasted nearly three years, federal prosecutor John Durham concluded that he would not bring a criminal case against the CIA officers. The burning of the 92 tapes on Nov. 9, 2005, was authorized in a cable sent by Jose Rodriguez Jr., head of the agency's directorate of operations.

The tapes showed the interrogations of two high-profile detainees. Sources have said they depicted waterboarding, a form of simulated drowning that human rights groups and Obama administration officials say is torture.

"As a result of that investigation, Mr. Durham has concluded that he will not pursue criminal charges for the destruction of the interrogation videotapes," Justice Department spokesman Matthew Miller said.

Yet even as the government closed one chapter in the investigation of Bush administration interrogation practices after the Sept. 11, 2001, attacks, other parts of the probe remained open. Sources familiar with Durham's investigation said authorities have not ruled out filing charges against officials who may have misled investigators during the probe into the tapes' destruction.

Durham is also conducting a related, and potentially more explosive, investigation into whether CIA employees and contractors broke the law in conducting interrogations at "black site" prisons. Sources said that probe remains active.

The political debate over whether the Bush administration violated civil rights in the years after Sept. 11 or was only trying to protect Americans also showed no signs of ending. In an interview Monday with NBC News, former president George W. Bush defended the waterboarding of terrorism suspects. On Tuesday, human rights groups criticized the Justice Department's decision in the CIA videotapes case and cited what they called Bush's legacy of torture.

"This decision is stunning: There is ample evidence of a coverup regarding the destruction of the tapes,'' ACLU Executive Director Anthony D. Romero said. "The Bush administration was instructed by a court of law not to destroy evidence of torture, but that's exactly what it did.''

C. Dixon Osburn, a spokesman for Human Rights First, said members of the group are "disappointed that the Justice Department has chosen not to pursue charges in this case" but "remain hopeful" that Durham's pending inquiries will produce criminal charges.

CIA Director Leon E. Panetta said that he welcomed the news and that the agency has cooperated with Durham's investigation from the start. "We will continue, of course, to cooperate with the Department of Justice on any other aspects of the former program that it reviews,'' he said.

But a former senior CIA operations officer, speaking on the condition of anonymity in order to comment freely, questioned the decision not to bring charges and said the tapes were not destroyed "in total innocence."

"To my understanding . . . there was a standing order from a federal judge that said not to destroy the tapes. That trumps any inside the CIA legal call," the ex-official said.