After leaving the administration, Berger was in the news in 2005 when he was fined and sentenced to community service
for removing classified documents from the National Archives.
In a statement, President Barack Obama called Berger "one of our nation's foremost national security leaders."
"I'm grateful to Sandy because, as President, I've benefited personally from his advice and counsel," the President said.
Berger had been battling cancer, according to a statement released by the Albright Stonebridge Group, the international advisory firm Berger co-founded in 2001.
"Our country is stronger because of Sandy's deep and abiding commitment to public service, and there are countless people whose lives he changed for the better," said ASG co-chair Madeleine Albright.
"He was one of my dearest friends and among the wisest people I have ever met. I will always treasure our decades-long partnership, both in and out of government, and I will be forever proud of what we accomplished together," she added.
While preparing to testify before the 9/11 commission, Berger improperly removed classified documents from the National Archives by stuffing them down his pants. After the removal became public, Berger told reporters that he had made an "honest mistake."
"I deeply regret the actions that I took at the National Archives two years ago, and I accept the judgment of the court," Berger said outside the courthouse after his sentencing.
Last month, Berger was awarded the Japanese government's Grand Cordon of the Order of the Rising Sun "for his significant contributions to strengthening the relations between the United States and Japan." Previous recipients of the award include House Democratic Leader Nancy Pelosi.
Earlier this week, the World Food Program honored him with the first Global Humanitarian Award. The WFP also created the Samuel R. Berger Humanitarian Fund, which will focus on humanitarian responses to conflict.
Berger served as Clinton's second-term National Security Advisor and helped formulate the administration's foreign policy. Prior to that, he was Deputy National Security Advisor during the first term and had advised Clinton on foreign policy during his presidential campaign.
He also served as a foreign policy advisor to Hillary Clinton in her 2008 presidential campaign.
Berger is survived by his wife, Susan, and three children.