"We still have a fight on our hands," Panetta said Sunday on ABC's "This Week."
"The American people need to know that. The world needs to know that ... but we're on the right track," he added.
Last week, NATO allies affirmed a plan to end combat operations inside Afghanistan by the end of 2014. Republicans, including Mitt Romney, have criticized President Barack Obama's insistence on setting a firm timetable for the war because they say it shows a lack of commitment to the region and encourages enemy fighters to wait out a U.S. departure.
Panetta said critics of the plan should be mindful that the timetable has been embraced by some 50 allied nations.
"That is the plan that has been agreed to. And it's a plan that is working," Panetta said.
"And very frankly, the only way to get this accomplished - in terms of the transition that we have to go through - is to be able to set the kind of timelines that have been set here in order to ensure that we fulfill the mission of an Afghanistan that governs and secures itself," he added.
Panetta also reiterated his criticism of the conviction of a Pakistani doctor who helped the CIA find and kill terrorist leader Osama bin Laden, calling the lengthy prison sentence handed to Dr. Shakil Afridi "disturbing."
"It is so difficult to understand and it's so disturbing that they would sentence this doctor to 33 years for helping in the search for the most notorious terrorist in our times," Panetta said. "This doctor was not working against Pakistan."
U.S. officials have urged Pakistan to release the physician, who ran a vaccination program for the CIA to collect DNA and verify the al-Qaida leader's presence at the compound in the town of Abbottabad where U.S. commandos killed him in May 2011.
The capture of bin Laden strained the U.S. relationship with Pakistan, as did U.S. airstrikes that accidentally killed 24 Pakistani soldiers near the border. Pakistan responded to the airstrikes by closing key transit routes into Afghanistan. The chilly U.S.-Pakistan relationship was on public display at last week's NATO meeting, where Obama left Pakistan off a list of nations he thanked for help getting war supplies into Afghanistan.
Panetta called the U.S. relationship with Pakistan "one of the most complicated we've had."
"This is a country that still is critical in that region of the world," he said. "It's an up-and-down relationship. There have been periods where we've had good cooperation and they have worked with us."
