"In the 21st century, the reality is that there are environmental threats which constitute threats to our national security," Panetta said in a speech in Washington this week to the Environmental Defense Fund.
He cited rising sea levels, severe droughts, the melting of the polar caps and more frequent and devastating natural disasters, all of which he said raise demand for humanitarian assistance and disaster relief.
As one of the largest landowners and energy consumers in the world, he said, the U.S. Department of Defense is striving to be more efficient and environmentally sustainable.
He also expressed concern about electrical power-related threats to the nation's security.
"I have a deep interest in working to try to ensure from a security perspective that we take measures that will help facilitate and maintain power in the event of an interruption of the commercial grid that could be caused, for example, by a cyberattack which is a reality that we have to confront," he said.
The quest for energy is another area, he said, that continues to shape and reshape the strategic environment, "from the destabilizing consequences of resource competition to the efforts of potential adversaries to block the free flow of energy.
"These strategic and practical considerations weighed heavily on us as we developed our new defense strategy."
The Pentagon, which accounts for more than 1 percent of U.S. energy consumption, spent more than $17 billion on fuel last year.
In the past half century, the amount of fuel needed to support deployed U.S. service personnel has risen from 5 gallons a day per person to more than 22 gallons, says a study by Pew Charitable Trusts.
Panetta said the Department of Defense faces a budget shortfall of more than $3 billion due to higher than expected fuel costs this year.
In March the Pentagon unveiled a plan to reduce fuel consumption and to promote energy efficiency across all branches of the military. It sets seven specific targets for "transforming the way U.S. armed forces consume energy in military operations."
For its 2013 budget, the Pentagon is requesting more than $1 billion for efficient aircraft and aircraft engines, hybrid electric drives for ships, improved generators and micro-grids for forward-deployed bases and combat vehicle energy efficiency programs.
Another $1 billion is sought for energy improvements at military installations in the United States.
Panetta said the U.S. Army, U.S. Navy and U.S. Air Force have committed to adding about 3 gigawatts of renewable energy to installations in the coming years, which he said was one of the largest commitments to clean energy in the nation's history.
"We are working to be a leader and a bold innovator in environmental stewardship, energy efficiency and energy security," Panetta said.