ISLAMABAD, Pakistan - Will Pakistani assistance to Afghan militants doom America's efforts in Afghanistan?

This question continues to haunt the Afghan conflict in a week when President Obama is releasing a review of war strategy and mourning the death of his top civilian envoy to the region, Richard Holbrooke.

Two new U.S. intelligence estimates contend that success is unlikely so long as Pakistan permits Afghan militants to find sanctuary in its border areas. Add to this the long-standing claims, fueled anew by WikiLeaks documents, that Pakistan's spy agency is duping its American ally by aiding militants while the country is hauling in $1 billion a year in U.S. military aid.

So expect congressional calls for harsher pressure on Islamabad.

Yet a trip here with the chairman of the joint chiefs, Adm. Mike Mullen, presents a very different picture. Despite constant frustrations, top U.S. military officials don't believe threats will get results here. They are determined to slog away at building trusting relationships with their Pakistani counterparts that may produce a better outcome in the long run.

This may be a hard sell in Washington. Yet the approach of Mullen and other military officials makes painful sense because it recognizes hard realities on the ground.

"Sanctuaries [in Pakistan] are a priority," Mullen told a small group of journalists on a flight from Baghdad to Islamabad. "[Pakistani army chief Ashfaq Parvez] Kayani is aware of this and we constantly address this." He's held 21 meetings in the past three years with Kayani in Pakistan and several meetings elsewhere. Gen. David Petraeus and other top brass have also held frequent confabs with the Pakistani military leader.

Although Mullen recognizes the need for short-term results, he is focused on the long term, trying to align U.S. and Pakistani objectives to the greatest extent possible. Until 2007, those objectives diverged greatly: Pakistan's military was ready to cut deals with some militants; it viewed Afghan Taliban groups as a hedge in its long-running conflict with India.

However, in the last two years, the Pakistani military has been forced to confront militants after they began to attack government and military installations. Mullen points to progress: Kayani has transferred large numbers of troops from the Indian border to the border with Afghanistan, waged substantial campaigns against militant groups, and taken heavy casualties.

U.S. military trainers, once unwelcome, now work extensively with Pakistanis, especially with the Frontier Corps, which guards the Afghan border. Cooperation with U.S. and Afghan troops on sealing the border is improving.

However, the Pakistani military is still focused on fighting Pakistani Taliban and has not confronted Afghan militants such as the Haqqani group in North Waziristan, the scourge of U.S. forces in eastern Afghanistan. For critics, this is evidence that the Mullen strategy won't work.

Yet Mullen still believes he can convince his Pakistani counterpart that, when it comes to confronting militancy, his interests are parallel to America's. He tells Kayani that all militant groups are linked in one syndicate that also threatens Pakistan.

"I've been very clear in my conversations with General Kayani," Mullen told a group of Pakistani journalists. "There needs to be focus on North Waziristan.

"General Kayani," he added, "has spoken of this in terms of 'not if but when.' "

However, Kayani's forces are overstretched, all the more so because a devastating flood diverted thousands of his men and vital military transport. The worst-case scenario, U.S. military officials say, would be for Kayani to move against the Haqqanis before his military has enough capacity - and lose.

That raises the question of whether Kayani will ever make that move. Yes, he will, says a U.S. defense official here, "so long as we are patient." Many Pakistani officers serving on the Afghan border are already changing their thinking, he says, especially now that they understand that U.S. troops won't all be leaving Afghanistan in 2011.

This defense official also suggested that there may be too much focus on North Waziristan as a magic bullet that will determine the outcome in Afghanistan. "In Iraq, we thought we couldn't win because of sanctuaries in Syria, but [that] turned out to be less true than we thought," he said.

So Mullen and military officials here will keep their focus long-term - despite the skeptics - even as they urge Kayani to do more. Is it possible Kayani is not getting the message? "I think he's getting it loud and clear," the chairman replied.

We will see next year.