Clinton said the independent probe would help establish the rule of law in the war-torn nation that had been ruled as a dictatorship by Gadhafi for decades.
"I think that the new Libya needs to start with accountability, the rule of law, a sense of unity and reconciliation in order to build an inclusive democracy," Clinton said on ABC's "This Week."
"People who supported the former regime -- unless they do have blood on their hands -- should be safe and feel included in this new country."
Clinton added not all was forgiven. She said the United States would continue to press for the return of convicted Pan Am 103 bomber Abdelbaset Ali al-Megrahi, who was freed from prison in Scotland in 2009 because he was supposedly about to die of cancer. "We want to see him returned to prison, preferably in Scotland, where he was serving the sentence," she said.
Clinton said one of the United States' current Middle East adversaries, Iran, would not be moving into Iraq to fill a presumed security vacuum caused by the imminent departure of U.S. forces.
She told CNN's "State of the Union" U.S. forces would remain in country to help train Iraq's military. "We have a lot of presence in that region," Clinton said. "So no one, most particularly Iran, should miscalculate about our continuing commitment to and with the Iraqis going forward."
Clinton disagreed with Republican criticism of the accelerated Iraq withdrawal, saying on "Fox News Sunday" the plan dating back to the Bush administration was to set Iraq on the path to stable democracy and then leave. "The point of our involvement in Iraq stated over and over again by people on both sides of the aisle was to create the opportunity for the Iraqis to have their own future," she said.
Clinton cited Iraq and Libya as examples of the Obama administration's seemingly adroit handling of ticklish foreign policy issues.
"I think this president has demonstrated that in a still very dangerous world it's important to have someone at the helm of our country who understands how to manage what is an incredibly complex world now," she said on NBC's "Meet the Press".
"Yes, we have a lot of threats, but we also have opportunities and I think President Obama has grasped that and has performed extraordinarily well."