The CIA is facing a potentially crippling loss of human intelligence from foreign militant groups because some of its best spies in the field are unwilling to work for US President Donald Trump's administration, Middle East Eye has learned.

Contracted agents, some of whom run networks of sources within al-Qaeda and the Islamic State (IS) group have either quit or threatened to quit amid frustration in the intelligence services since Trump took office last month.

These operatives are known as "terrorist hunters" and are both American and other nationalities. They are mostly Muslim and some are allowed to develop their own assets and run their own big budgets.

This is going to be the largest loss in intelligence history in the fight against terrorism.

Some were recruited almost a decade ago for their strength and motivation and have track records of providing genuine plot-busting intelligence.

"This was the generation of operatives who came about after the restructuring after George W Bush, to reclaim their credibility, to focus on the facts and not to massage them. Now they believe they are going to go back to square one," a source with knowledge of the resignations told MEE.

"The ramifications on society in the US and Europe will be substantial. These are people who know the terrain and who blend in. Some of them have been undercover for years. Now they all sent a message to Washington: 'We are quitting'."

The threatened resignation of two "terrorist hunters" in particular is a source of concern at the CIA's Langley headquarters, the source added.

"They are irreplaceable. Them quitting the business will harm the interests of the US. These two guys are responsible for 50 to 60 percent of the pre-emption of terrorist attacks you never hear about," the source said.

According to the source, the two agents were quitting for two main reasons.

Sources said Trump's idiological bias had taken them back to 'square one' (AFP)

As loyal Americans, they are disgusted by the low intellectual calibre of the leaders they now have to serve as well as their ideological bias against, and suspicion of Muslims in general.

They are frustrated by the new intelligence chiefs' ignorance of Islam, their inability to differentiate between different groups of Salafi-jihadists, and their propensity to lump all Islamist groups, both violent and non-violent, into one pot.

But as intelligence operatives, they are also concerned about a shift in priorities away from IS and al-Qaeda, to focus instead on ideological issues which are irrelevant to, or actively hamper, counter-intelligence.

They are "extremely concerned" that the leadership of the intelligence community has been put in the hands of former military generals, and their primary concern is to protect their intelligence assets and prevent them from being used to serve political purposes.

The ramifications will be substantial. These are people who know the terrain and blend in. Some have been undercover for years.

They also are worried that Trump's comments about wanting to see a return of waterboarding will become a huge recruiting tool for IS.

Mike Pompeo, who was confirmed as the CIA's new director by Congress, had said he would consider bringing back waterboarding and other "enhanced interrogation techniques" under certain circumstances.

But during his Senate confirmation hearing, he dismissed the idea he would bring back torture as CIA chief.

In 2013 Pompeo claimed Muslim American leaders did not speak out enough against terror attacks and could, therefore be "potentially complicit" in those attacks.

An expert with a close working knowledge of "radical Islamic groups" in the region told MEE: "This is going to be the largest loss in intelligence history in the fight against terrorism. It will take years to rebuild the network and the people and the new assets.

"The only way to stop this is by appointing people who are known to be knowledgeable, rational, and non-political."

A source said it would take years to rebuild networks that had infiltrated groups such as Islamic State (AFP)

The CIA denied that agents are leaving the agency because of the new administration.

"CIA continues to carry out its mission and does so with the highest degree of professionalism and competence," CIA spokesman Ryan Trapani told MEE via email.

"There has been no spike in officers leaving the agency since the inauguration. Gossip suggesting the contrary is wrong."

However, there has been a rising chorus of corroboration of the strains developing within the US intelligence community.

Edward Price who worked at the CIA from 2006 revealed in the Washington Post newspaper earlier this week that he had quit because of growing demoralisation within the organisation over Trump.

Price wrote that Trump's actions in office had been even more disturbing than his trashing of the "high confidence" conclusion of 17 intelligence agencies that Russia was behind the hacking and release of election-related emails.

Trump's visit to the CIA, where he continued to brag about his election victory rather than address the audience, was another cause for concern.

There has been no spike in officers leaving the agency since the Inauguration. Gossip suggesting the contrary is wrong - CIA spokesman Ryan Trapani

"Whether delusional or deceitful, these were not the remarks many of my colleagues and I wanted to hear from our new commander in chief," said Price.

"I couldn't help but reflect on the stark contrast between the bombast of the new president and the quiet dedication of a mentor - a courageous, steadfast professional - who is memorialised on that wall. I know others at CIA felt similarly."

The final straw for Price was the directive reorganising the National Security Council (NSC), on which he served, earlier this year: "Missing from the NSC's principals committee were the CIA director and the director of national intelligence. Added to the roster: the president's chief strategist Stephen K Bannon, who cut his teeth as a media champion of white nationalism."

Leon Panetta, a former CIA director, warned specifically about the dangers of Trump's executive order to ban refugees and travellers from seven Muslim-majority countries in an affidavit lodged with the US Court of Appeal to Ninth Circuit, which upheld the stay on the executive order.

"The order will disrupt key counterterrorism, foreign policy, and national security partnerships that are critical to our obtaining the necessary information sharing and collaboration in intelligence, law enforcement, military, and diplomatic channels to address the threat posed by terrorist groups such as ISIL [IS]," the affidavit said.

"The international criticism of the order has been intense, and it has alienated US allies.

"It will strain our relationships with partner countries in Europe and the Middle East, on whom we rely for vital counterterrorism cooperation, undermining years of effort to bring them closer.

"By alienating these partners, we could lose access to the intelligence and resources necessary to fight the root causes of terror or disrupt attacks launched from abroad, before an attack occurs within our borders."

The affidavit also was signed by former secretaries of state Madeleine Albright, John Kerry, and Janet Napolitano, a former secretary of homeland security.

This article is available in French on Middle East Eye French edition.