Defense Secretary Leon E. Panetta expressed confidence today that the United States and Pakistan can patch up their differences, emphasizing that “ultimately, we can’t win the war in Afghanistan without being able to win in our relationship with Pakistan as well.”

The secretary said restoring the strained relationship with the United States critical to long-term progress in Afghanistan. “I think it is going to be important, as we are able to move and progress in our efforts in Afghanistan, that we continue to do outreach in Pakistan,” he said.

“It is essential to stability in that region that we not only achieve a peaceful resolution with regards to Afghanistan, but that we are able to develop a more stable relationship with Pakistan as well,” he said. “If that region is ever going to find peace, it is going to happen not only by achieving stability in Afghanistan, but also by achieving some degree of stability in Pakistan as well.”

The U.S. relationship with Pakistan has been “difficult and complicated,” Panetta conceded. “But it is an important relationship, and it is one we have to continue to work at.”

The secretary noted that Pakistan has provided important cooperation to the United States. “At the same time, we have had some serious difficulties with regards to some of the operations that involve groups in the FATA [federally administered tribal areas] and groups along the border,” he said.

Strain between the two countries increased after the May 2 raid that took down Osama bin Laden in Pakistan, and intensified after a Nov. 26 engagement near Pakistan’s border with Afghanistan that killed 24 Pakistani soldiers.

U.S. Central Command is conducting a full investigation of the incident, under the leadership of Air Force Brig. Gen. Stephen A. Clark from Air Force Special Operations Command.

“A number of interviews have been conducted,” to determine factors involved in the incident, Panetta said. He expressed hope that the investigation will shed light on “exactly what happened,” but said he has not yet received an update on any findings.

Meanwhile, Panetta said Marine Corps Gen. John Allen, commander of U.S. and ISAF forces in Afghanistan, reports that operations are continuing to secure the border areas.

Even before the border incident, Allen reached out to Pakistani Army Chief of Staff Gen.Ashfaq Parvez Kayani to develop a relationship that would allow the United States and Pakistan to better coordinate and control border-area operations to prevent incidents, he said.

“Obviously what took place has complicated that relationship,” Panetta said. “But I think the effort now is to try to see if we can restore that kind of communication with regards to those border incidents.”

The United States also is working to get Pakistan to reopen ground supply routes into Afghanistan it closed after the border incident. “I am confident that will happen,” Panetta said. “I remain confident that at one point, we are going to be able to restore our normal supply routes.”

For now, Panetta said he’s satisfied that troops have the supplies they need to continue their operations in Afghanistan. “Our command structure has done an incredible job ensuring that one way or another, we are able to get those supplies in,” he said.

Ultimately, restoring a solid relationship goes well beyond supply routes and border operations, the secretary said.

And if there’s one thing he said he’s learned, both at CIA and at the Defense Department, it’s the need to continue working at the relationship, even through “bumps in the road” and crises.

“The most important thing is to keep lines of communication open and make sure we do everything we can to restore some degree of a relationship that will allow us to be able to fulfill our mission,” he said.

Panetta emphasized that the mission of confronting terrorism supports both the United States’ and Pakistan’s interests.

“The terrorism that threatens us also threatens them,” he said. “And if we can recognize that, despite our differences, there are some common areas that we share in terms of our security, then I think we can ultimately find a way to resolve our differences and improve our relationship,” he said.

The secretary also spoke about President Barack Obama’s request that Iran return a recovered U.S. RQ-170 drone aircraft to the U.S., saying the request was “appropriate.” However, the secretary admitted that he didn’t “expect that will happen.”

Panetta said it’s difficult to know how much engineering know-how the Iranians will be able to obtain from parts of the downed drone in its possession. “I don’t know the condition of those parts. I don’t know exactly what state they are in,” he said. “So it will be a little difficult to tell exactly what they are going to be able to derive from what they have been able to get.”