A senior U.S. official said they were concerned about al Qaeda leaders in remote areas of the country and there may be many more core operatives in Afghanistan than previously thought.
The warnings of al Qaeda's resurgence come as Afghanistan faces perhaps the most significant summer fighting season in decades, with government security forces facing huge internal challenges
, the Taliban both gaining ground
and building links to al Qaeda, and ISIS increasing its footprint in the country
Acting Defense Minister Masoom Stanikzai told CNN that al Qaeda were keeping a low profile but expanding.
"They are really very active. They are working in quiet and reorganizing themselves and preparing themselves for bigger attacks," he said.
"They are working behind other networks, giving them support and the experience they had in different places. And double their resources and recruitment and other things. That is how -- they are not talking too much. They are not making press statements. It is a big threat."
Major General Jeff Buchanan, Deputy Chief of Staff for the U.S. military presence in Afghanistan, said the recent discovery and destruction of an al Qaeda training camp in Kandahar province meant previous U.S. estimates of the group's strength were being revised.
"If you go back to last year, there were a lot of intel estimates that said within Afghanistan al Qaeda probably has 50 to 100 members, but in this one camp we found more than 150."
He admitted there was a gap in U.S. knowledge of the problem, and warned the group's core focus was still attacking the West.
"There's not thousands of them, but clearly in remote parts of Afghanistan there are al Qaeda leaders we're concerned about and what they're capable of doing."
U.S. officials said the number of core al Qaeda operatives in Afghanistan could be as high as 300, but that number does include other facilitators and sympathizers in their network.
'They need the fighters'
The now-destroyed training camp
-- attacked in a lengthy operation by U.S. special forces and Afghan commandos in October -- showed a high degree of sophistication "with ties back to al Qaeda and a subset called al Qaeda in the Indian Subcontinent," Buchanan said.
"To find them in Afghanistan was quite troubling."
Al Qaeda in the Indian Subcontinent has not previously been associated much with Afghanistan. The discovery of any presence of them in the country raises concerns Afghanistan is once again becoming a safe haven for international terrorist networks whose main focus is attacks outside Afghanistan, including the West.
The Afghan militant group was thought to have regretted its decision to harbor Osama bin Laden before the September 11, 2001 terrorist attacks, because it led the U.S. to launch a war to remove them from power.
Yet since Mullah Akhtar Mohammad Mansour
became leader in mid-2015, the group has grown closer to al Qaeda. The Taliban's current deputy commander, Siraj Haqqani, is the head of the feared Haqqani militant network and al Qaeda's top facilitator in Afghanistan, according to U.S. officials.
"The big cover is the Taliban," said Stanikzai.
"They need the fighters, they need the support and they need recruitment from other places, and this is why (the Taliban)
U.S. General John Campbell, former commander in Afghanistan, has referred to a "renewed partnership between the two groups. Buchanan said the relationship has since "grown stronger."
This burgeoning partnership poses a problem for any attempt by the U.S. and Afghan governments to negotiate a political settlement with the Taliban.
Official U.S. policy is that the militant group must renounce international terrorism before any talks begin. Yet analysts fear the opposite is occurring, with the Taliban-al Qaeda relationship only growing stronger.
The Taliban have also openly stated they are not currently interested in peace talks, though U.S. and Afghan officials insist some moderates do want to talk.
"Many leaders in the Taliban are willing to enter into constructive peace talks," Stanikzai said.
"From a military point of view, we have to have the flexibility to target them. When it comes to negotiation, you cannot just burn everything."