NEW YORK - Al Qaeda training camps have sprouted up in Afghanistan, according to a leading American newspaper which said that reappearance of the “old enemy” was leading to questions on whether they could again become breeding grounds for attacks on the United States.

The report of the new camps comes as the Obama administration scrambles to confront the Islamic State and resurgent Taliban, The New York Times said in a dispatch on Tuesday. Although most of the handful of camps were not as big as those that Osama bin Laden built before the 9/11 attacks, the Times said Al Qaeda’s “deadly” resilience in Afghanistan appears to have caught American and Afghan officials by surprise. Until this fall, it said, American officials had largely focused on targeting the last remaining senior Qaeda leaders hiding along the Pak-Afghan border.

The newspaper said the administration has said little about the new challenge or its strategy for confronting the threat from Al Qaeda, even as it rushes to help the Afghan government confront what has been viewed as the more imminent threat, the surge in violent attacks from the Taliban, the Haqqani network and a new offshoot of the Islamic State. Former administration officials, it said, have been more outspoken - especially those who were on the front lines of the original battle to destroy Al Qaeda’s central leadership.

“I do worry about the rebirth of AQ in Afghanistan because of what their target list will be - us,” Michael Morell, the deputy director of the C.I.A. until two years ago, was quoted as saying.

“It is why we need to worry about the resurgence of the Taliban,” Morell said, “because, just like before, the Taliban will give Al Qaeda a safe haven.”

But a senior administration official was cited as saying that the increased Qaeda activity was more the result of Pakistani military operations pushing fighters across the border into Afghanistan than Qaeda enlisting new Afghan recruits inside the country.

In October, American and Afghan commandos, backed by scores of American airstrikes, attacked a Qaeda training camp in the southern part of the country that military officials said was one of the largest ever discovered.

The assault, which took place over several days, pounded two training areas - one sprawled over 30 square miles - that featured elaborate tunnels and fortifications. As many as 200 fighters were killed, American officials said.

Senior administration officials say that there are other Qaeda camps or bases, including at least one in Helmand Province, though they are not certain exactly how many because they were made harder to detect after the October assault. The senior officials - four from three different federal agencies - spoke on the condition of anonymity to discuss confidential intelligence assessments.

A spokesman for the United States military in Afghanistan, Col. Michael Lawhorn, declined in an email to discuss “any current intelligence we may have on Al Qaeda training camps,” according to the newspaper.

The two camps attacked in the fall were in a sparsely populated area of Kandahar Province. Some of the facilities apparently were in place for up to a year and a half, undetected by American or Afghan spies or surveillance aircraft.

“A lot of that is because, you know, it’s a very remote part of Kandahar,” General John Campbell, the top American commander in Afghanistan, was quoted as saying.

For months, the Times said, General Campbell has been sounding a warning about Al Qaeda in the broader context of Afghanistan’s complex threat environment, telling Congress in October that Afghan security forces “have thus far proven unable to eradicate Al Qaeda entirely.”

“Al Qaeda has attempted to rebuild its support networks and planning capabilities with the intention of reconstituting its strike capabilities against the U.S. homeland and Western interests,” General Campbell said in his testimony.

The general said that pressure on Qaeda fighters from the United States and its Afghan allies had forced them to be “more focused on survival than on planning and facilitating future attacks,” but that continued pressure was necessary to keep Al Qaeda from gaining new footholds.

The discovery of the large camp attacked in October raised questions about the American military’s ability to detect and destroy a major Qaeda stronghold in the country, more than 14 years after the American-led invasion of Afghanistan drove out Al Qaeda and toppled the Taliban government that supported them, according to the dispatch.

General Campbell said at the time of the October raid that the camp was used by a new Qaeda offshoot called Al Qaeda in the Indian Subcontinent, or AQIS. Ayman al-Zawahri, Al Qaeda’s overall leader, announced the creation of the affiliate in September 2014 largely in response to the rise of its rival, the Islamic State, which is also known as ISIS or ISIL.

AQIS fighters began migrating from sanctuaries in North Waziristan and eastern Afghanistan to the country’s southern provinces of Helmand and Kandahar last year, after Pakistan launched a military offensive in the region, said Seth Jones, an Afghanistan specialist at the RAND Corporation. Kandahar and Helmand have not typically been havens for Al Qaeda.“It’s been a relatively recent expansion to the south,” Jones said.

Afghan security officials say many of these foreign fighters filtering in are from Central Asia, and in many cases their affiliations are unknown. In the past, some of the groups have been affiliated with Al Qaeda, but there have also been reports of some of these fighters pledging allegiance to the Islamic State.

It said one American intelligence official sought to play down the menace from the new Qaeda offshoot, calling it “a regional threat that is currently focusing on plotting attacks in Pakistan and establishing a presence in South Asia. Despite its safe haven, the group has not been seen conducting attacks against Afghan or Western targets in Afghanistan.”

The emergence of new Qaeda training camps comes amid a widespread erosion in security in much of the country. “In the second half of 2015, the overall security situation in Afghanistan deteriorated, with an increase in effective insurgent attacks and higher A.N.D.S.F. and Taliban casualties,” the Pentagon said in a report issued two weeks ago, using the initials for the Afghan National Defense and Security Forces.

General Campbell told lawmakers that the Haqqani network, remains an important “facilitator” for Al Qaeda in Afghanistan. The two groups, he said, share a goal of “expelling coalition forces, overthrowing the Afghan government, and re-establishing an extremist state.”

Rounding out the threats in Afghanistan, General Campbell told lawmakers that the Islamic State’s branch in the country was rapidly drawing new fighters with its “virulent, extremist ideology.”

“While many jihadists still view Al Qaeda as the moral foundation for global jihad, they view Daesh as its decisive arm of action,” he said, using another name for the Islamic State. Citing a remark by the Afghan president, Ashraf Ghani, General Campbell said, “If Al Qaeda is Windows 1.0, then Daesh is Windows 7.0.”