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In late September, U.S. fighter jets streaked over the cedar-studded slopes of Korengal, the so-called Valley of Death, to strike a target that hadn’t been seen for years in Afghanistan: an al Qaeda training camp.

Among the dozens of Arabs killed that day, the U.S.-led coalition said, were two senior al Qaeda members, one Saudi and the other Kuwaiti. Another casualty of the bombing, according to Saudi media and jihadi websites, was one of Saudi Arabia’s most wanted militants. The men had come to Afghanistan to impart their skills to a new generation of Afghan and foreign fighters.

Even though the strike was successful, the very fact that it had to be carried out represents a troubling shift in the war. Nine years after a U.S.-led invasion routed almost all of al Qaeda’s surviving militants in Afghanistan, Osama bin Laden’s network is gradually returning.

Over the past six to eight months, al Qaeda has begun setting up training camps, hideouts and operations bases in the remote mountains along Afghanistan’s northeastern border with Pakistan, some U.S., Afghan and Taliban officials say. The stepped-up infiltration followed a U.S. pullback from large swatches of the region starting 18 months ago. The areas were deemed strategically irrelevant and left to Afghanistan’s uneven security forces, and in some parts, abandoned entirely.

American commanders have argued that the U.S. military presence in the remote valleys was the main reason why locals joined the Taliban. Once American soldiers left, they predicted, the Taliban would go, too. Instead, the Taliban have stayed put, a senior U.S. military officer said, and “al Qaeda is coming back.”

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The militant group’s effort to re-establish bases in northeastern Afghanistan is distressing for several reasons. Unlike the Taliban, which is seen as a mostly local threat, al Qaeda is actively trying to strike targets in the West. Eliminating its ability to do so from bases in Afghanistan has always been the U.S.’s primary war goal and the motive behind fighting the Taliban, which gave al Qaeda a relatively free hand to operate when it ruled the country. The return also undermines U.S. hopes that last year’s troop surge would beat the Taliban badly enough to bring them to the negotiating table—and pressure them to break ties with al Qaeda. More than a year into the surge, those ties appear to be strong.

To counter the return, the coalition is making quick incursions by regular forces into infiltrated valleys—”mowing the grass,” according to one U.S. general. It is also running clandestine raids by Special Operations Forces, who helped scout out the location of the Korengal strike, U.S. officials said. The twin actions offer a preview of the tactics the coalition is likely to pursue in some parts of the country as its forces hand off chunks of contested territory to Afghanistan’s security forces. The process is already under way and is due to accelerate in July.

Precise numbers of al Qaeda fighters in Afghanistan at any given time are hard to come by. But officials say al Qaeda camps and gathering spots similar to the one targeted in September are now scattered across sparsely populated Kunar province, a few inaccessible parts of Nuristan province and, most worryingly to some officials, the edges of Nangarhar province. That province sits astride a major overland route from Pakistan and is home to one of Afghanistan’s major cities, Jalalabad.

For the most part, al Qaeda has been viewed by Western officials as a declining force in the Afghan fight. Just six months ago, U.S. intelligence estimates indicated only one or two dozen al Qaeda fighters were present in Afghanistan at any given time. Most of the few hundred fighters it had in the region were holed up in Pakistan, hiding from Central Intelligence Agency drone strikes in mountain shelters, and beset by morale and money problems. Some fighters would occasionally cross the border to conduct training or embed with Taliban units, a pattern that had become well established over a decade of war.

Now, the U.S. pullback from northeastern Afghanistan appears to have given al Qaeda the opening it needed to re-establish itself as a force in the Afghan fight, say some U.S. and Afghan officials.

“Al Qaeda tends to navigate to areas where they sense a vacuum,” said Seth G. Jones, a senior political scientist at Rand Corp. in Washington who has spent much of the past two years in Afghanistan advising the U.S. military. “There are serious concerns about al Qaeda moving back into some areas of Afghanistan, the places that we’ve pulled back from.”

Al Qaeda’s message of Islamic revolution has in recent months seemed increasingly out of sync in a Middle East where a series of grass-roots upheavals are being driven largely by secular young people demanding democracy. But its recent resurgence in Afghanistan suggests that it retains potency in predominately Muslim parts of South Asia where it has put down roots in the past 15 years.

Last year’s surge of 30,000 U.S. forces, authorized by President Barack Obama, aimed to inflict enough pain on the Taliban that they would negotiate a peace settlement on terms acceptable to the West. Coalition commanders and civilian officials were initially bullish about the new strategy’s chances, seizing on reports from Taliban detainees that a “wedge” was developing between al Qaeda and midlevel insurgent commanders. The insurgent leaders were said to be tired of fighting and increasingly resentful of what they considered the Arab group’s meddling in their fight.

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Associated PressU.S. Army soldiers in Kolack.

The reappearance of al Qaeda fighters operating in Afghanistan undercuts those reports from detainees. “There are still ties up and down the networks…from the senior leadership to the ground level,” said a U.S. civilian official, citing classified intelligence.

Interviews with several Taliban commanders bear out that assessment. The commanders say the al Qaeda facilities in northeastern Afghanistan are tightly tied to the Afghan Taliban leadership. “In these bases, fighters from around the world get training. We are training suicide bombers, [improvised explosive device] experts and guerrilla fighters,” said an insurgent commander in Nuristan who goes by the nom de guerre Agha Saib and who was reached by telephone.

The two senior al Qaeda operatives killed in the September air strike—identified by coalition officials as Abdallah Umar al-Qurayshi, an expert in suicide bombings from Saudi Arabia, and Abu Atta, a Kuwaiti explosives specialist—are believed to have come across the border from Pakistan’s neighboring tribal areas with the aid of the Taliban in the wake of the American withdrawal

The wanted Saudi, Saad al Shehri, hailed from one of the most prominent Arab jihadi families, according to Saudi accounts and jihadi websites. Two of his brothers, including a former Guantanamo detainee, and several cousins were among the founders of al Qaeda’s Yemen-based network.

Coalition officials say the senior al Qaeda men were accompanied by one or two dozen lower-level Arab fighters. Their mission was to train locals and get into the fight themselves.

“The raid gave us insight that al Qaeda was trying to reestablish a base in Afghanistan and conduct some training of operatives, suicide attackers,” the senior U.S. military officer said. “They found a safe haven in Afghanistan.”

A raid in December netted another senior al Qaeda operative, Abu Ikhlas al-Masri, who has long operated in and around Kunar, said another U.S. official. His capture has provided intelligence about al Qaeda’s attempts to reestablish Afghan bases, said the official.

There is debate within the U.S. military and intelligence community about the scope of the al Qaeda problem in Afghanistan. The September strike was watched carefully and “was a big deal,” said another military official.

But that official and others said the numbers remain small enough to manage and that camps are, at worst, few and far between and largely temporary. And almost all U.S. and Afghan officials caution that al Qaeda isn’t yet secure enough in northeastern Afghanistan to use the area as a staging ground for attacks overseas.

Besides, the officials said, having al Qaeda on the Afghan side of the border—where American forces have far greater freedom to strike—rather than in Pakistan has its advantages. The officials said many of al Qaeda’s fighters are fearful of establishing too big or permanent a presence in Afghanistan because of the threat posed by U.S. and allied forces.

Kunar and eastern Nangarhar and Nuristan are strategic terrain, which is why U.S. forces first moved in a few years ago. The area is bisected by a web of infiltration routes—mountain passes, smugglers’ trails, old logging roads—from Taliban-dominated parts of Pakistan’s tribal areas, and the valleys channel insurgents into Jalalabad city. From there, it’s a few hours by car to Kabul—and an international airport—on one of Afghanistan’s better-paved roads. Islamabad, and another international airport, is a day’s drive in the other direction.

The area’s blend of ample hiding spots, readily traversable routes and a population historically wary of central authority have long made it a favorite for militants.

The first revolts against Afghanistan’s Soviet-backed communist regime began there in the late 1970s. In the past decade, it has become a haven for an alphabet soup of Islamist groups.

Apart from al Qaeda and the Taliban, two of the most potent Pakistani militant groups have a significant presence in Kunar—Jaish-e-Muhammad and Lashkar-e-Taiba, which orchestrated the 2008 attacks in Mumbai. There’s also the Tehrik-e-Taliban Pakistan, as the Pakistan Taliban are known, and the two other main Afghan insurgent factions, the Haqqani network and Hezb-e-Islami. Rounding out the scene is a smattering of militants from Central Asia, Chechnya and beyond.

Some of the valleys in Kunar “look like what we”—the U.S. and President Hamid Karzai’s government—”are trying to keep Afghanistan from becoming,” said Rangin Dafdar Spanta, Afghanistan’s pro-Western national security adviser.

The fight in the northeast is being waged openly by regular U.S. forces, which are now routinely sweeping through valleys in limited operations that ordinarily last a few days. The operations mostly target Taliban units but sometimes disrupt al Qaeda activities, too, military commanders say.

“There’s been several times that we’ll get intelligence that there’s going to be a gathering, whether it’s junior-level leadership, whether it’s Taliban, Haqqani or al Qaeda and if we can target those locations than we’re absolutely going to do that,” said Major Gen. John Campbell, the commander of NATO forces in eastern Afghanistan, in an interview.

More quiet—and more effective, many American officials say—is the U.S. military’s secretive Joint Special Operations Command, known as JSOC, which oversees elite units like the Army’s Delta Force and Navy Seal Team Six. The groups are working with Afghan intelligence and the Central Intelligence Agency to keep al Qaeda off balance in northeastern Afghanistan.

It was a JSOC operation that led to the capture of Mr. al-Masri, the al Qaeda veteran, in December.

The problem, say officials, is that JSOC, with a global counterterrorism mission that gives it responsibility for strikes in Somalia, Yemen, Iraq, Afghanistan and other trouble spots, is already stretched thin. Relying on it to police Afghanistan’s hinterlands as American forces pull out may be unrealistic, some officials said.

“We do not have an intelligence problem. We have a capacity problem. We generally know the places they are, how they are operating,” said the senior U.S. military official, speaking of al Qaeda. The problem “is our ability to get there and do something.”

—Habib Khan Totakhil contributed to this article.Write to Matthew Rosenberg at matthew.rosenberg@wsj.com