The interrogators used techniques like "waterboarding," or simulated drowning, which President Barack Obama and human rights advocates say is torture.
In a statement announcing the closing of the last two cases in the lengthy investigation, Attorney General Eric Holder said it "was limited to a determination of whether prosecutable offenses were committed and was not intended to, and does not resolve, broader questions regarding the propriety of the examined conduct."
Current and former CIA officials welcomed the decision. They have maintained that the program, begun after the September 11 al Qaeda attacks on New York and Washington, was conducted under guidelines issued by lawyers of the administration of former President George W Bush.
CIA Director David Petraeus sent a message to agency employees announcing the closing of the case and thanking them for cooperating with the investigation.
Human rights activists criticized the Justice Department decision.
"Attorney General Holder's announcement is disappointing because it's well documented that in the aftermath of 9/11 torture and abuse was widespread and systematic. These cases deserved to be taken more seriously from the outset," said Melina Milazzo of the group Human Rights First.
The inquiry originally was designed to probe the destruction of videotapes of interrogations by CIA personnel. A former official familiar with the tapes' contents said they depicted two suspects - Abu Zubaydah and Abd al-Rahim al-Nashiri - being subjected to waterboarding.
Expanded investigation
Three years ago, Holder expanded the probe to include the detention and interrogation of 101 militants alleged to have been held in custody by US authorities in the years after the attacks.
The videotapes portion of the investigation, conducted by John Durham, a Connecticut-based federal prosecutor, was closed in 2010 with no charges brought.
In June of last year, the Justice Department announced that only two of the 101 detention and interrogation cases that Holder asked Durham to review would be expanded into full-scale criminal investigations.
These investigations, government sources said, related to the deaths in CIA custody of one prisoner in Afghanistan and another in Iraq.
The Afghan detainee, Gul Rahman, died in 2002 while being held at a secret CIA facility known as the "Salt Pit."
The Iraqi detainee, Manadel al-Jamadi, died in 2003 while in CIA custody at Iraq's notorious Abu Ghraib prison. He allegedly had been beaten by US Navy SEALs.
People familiar with the investigation said that because the deaths occurred so long ago, there would have been legal and evidentiary problems pursuing any prosecutions.
A US official said the CIA or Pentagon could still pursue disciplinary proceedings against personnel who may have been involved in alleged abuses.
In November last year, Obama, commenting on a Republican presidential candidates' debate in which Congresswoman Michele Bachmann and businessman Herman Cain backed the use of waterboarding, said: "They're wrong. Waterboarding is torture."
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US justice department investigation's into detainees deaths is a joke. Makes it look like a third world country's justice department, dancing to the beat of the executive office.
I wish Pakistan had done the same instead of releasing militants en masse.