The most urgent issue facing the next president (beyond the economy) will be how to deal with a remote area along the Afghan-Pakistan border, the new haven for al-Qaida and radical jihadis.

“The most likely near-term attack on the United States” is likely to originate there, says Adm. Michael Mullen, chairman of the Joint Chiefs of Staff, the nation’s highest-ranking military officer. I discussed the problem with him last week as he flew back to Washington on an Air Force executive jet after speaking at the Wharton School of the University of Pennsylvania.

He had much on his mind: Afghanistan and Pakistan, Iranian expansion, the overstressed military, and the “rest of the world.” He is also preparing for a “time of vulnerability” during the presidential transition, when enemies may try to take advantage.

But the problem along the Afghan-Pakistan border, Mullen said, “is the one I’m most concerned about” for the near future. It will be “front and center” on the agenda of the next president.

That’s why Mullen has made six visits to meet with his Pakistani counterpart, Gen. Ashfaq Kayani, since Kayani took command in November 2007.

The border problem is far more complex than emerges from the sound bites at political debates. “It’s not just about (sending) additional combat forces to Afghanistan,” Mullen told the Wharton students, although more are needed.

Afghanistan has a weak government and economy, a huge opium trade, and an inadequate army. If those problems aren’t addressed, more troops won’t help.

But the root of the crisis lies in the havens on the Pakistani side of the border, from which Afghan Taliban attack their homeland, Pakistani extremists mount strikes, and al-Qaida plots against the West. Without those havens, Mullen said, “there would still be a significant challenge in Afghanistan, but the violence would be down.”

So why is it so hard to deal with the border problem? “We know the al-Qaida leadership is there,” Mullen told me. “But we recognize that the safe haven is in another sovereign country.”

In other words, we can’t just invade. The havens lie in a remote, mountainous, fiercely tribal region, which even the Pakistani military is reluctant to enter. The Pakistani public is hostile to the idea of its army attacking the militants. The army itself has been more oriented toward fighting its old enemy, India.

Many say they believe that elements in Pakistan’s military and Inter-Services Intelligence Agency are reluctant to fight some jihadi groups, which they once backed as a hedge against India. Mullen knows this history, but said he’s trying to understand present behavior. He commended Kayani for making “leadership changes,” including a new head of the ISI. Any future strategy toward Pakistan and Afghan-istan, he added, should work toward better Indian-Pakistani relations.

Mullen does think, however, that the Pakistani military’s outlook is shifting after horrendous terrorist attacks on targets in their own country. “I have great confidence that they understand they have a very serious threat on their hands,” he said.

Mullen said he was impressed by the Pakistani military’s recent major operation in Bajaur, a Taliban and al-Qaida tribal stronghold along the border. “That is consistent with what the Pakistani military told me they would do,” not because America pressed, but “because Pakistani leaders recognize the threat that they have.”

He was especially pleased that a tribal leader in Bajaur had mobilized several thousand anti-Taliban fighters. He hopes that other tribal leaders might do likewise. Think Anbar province in Iraq.

Yet it’s far from clear the Pakistani military has the skills it needs. Mullen said that, in a couple of weeks, 22 U.S. military experts would arrive to train Pakistanis, who would in turn train members of the Frontier Corps (an ineffective paramilitary that patrols the border). That’s a pretty small step.

“In the discussions I’ve had with Kayani,” Mullen said, “we are looking for ways to assist where they want to be assisted.” So far, the Pakistani army hasn’t asked for more counterinsurgency training. (It does want U.S. night-vision equipment and helicopters that, so far, haven’t been supplied.)

Neither can Mullen control the crucial Pakistani political piece of the puzzle. Pakistan’s new, elected, political leaders must convince the public that the war on insurgents is their war, not just a fight imposed by the United States. And the civilian government must also provide economic aid to tribal areas. Mullen commended Sens. Joe Biden and Richard Lugar for a plan to funnel more U.S. aid to civilians and tribes. But Pakistan’s new leaders are weak and disorganized, which makes military progress slower.

Pakistan and the United States are operating on different clocks. “The toughest variable to figure out,” Mullen said, “is time.”

A U.S. commander must worry about al-Qaida plots now. So the U.S. temptation is to send missiles or men across the border. A recent cross-border attack by U.S. special forces caused an uproar and turned the public further against Pakistan-U.S. cooperation. Vicious circle.

“When we have pursued (insurgents) in self-defense, we strain the relationship further,” Mullen said. “How do you protect the American people while recognizing this is a sovereign country? There is no precise answer … it depends on the growth and strength of this relationship.”

Mullen repeated the word relationship over and over. To him, the key to progress is establishing a relationship of trust with leaders of the Pakistani military that encourages them to cooperate with U.S. counterparts. That requires restoring the trust that was undercut when America cut off all military aid in the 1990s.

“I’ve got to look at these problems through the eyes of the people who live there,” Mullen told the Wharton students. “I have to be there, to listen. That’s why I’ve been there six times.” And why, no doubt, he’ll keep going back.

– Trudy Rubin is a columnist and editorial-board member for the Philadelphia Inquirer.