Experts say Flynn's claim, which was uncovered as part of a CNN KFile review of Flynn's past statements, shows a profound misunderstanding of education in the Middle East and expressed concern about how Flynn's views would affect his policy recommendations as the national security adviser to president-elect Donald Trump.
Flynn, a retired Army lieutenant general, made the comment in January during a seminar
hosted by the Endowment for Middle East Truth.
Arguing that Middle Eastern education systems were deficient because "most of their education now is in these madrasas," Flynn said, "It's an easy, it's sort of a, and, I'm sort being a little bit, but it's a poor man's school. You know? Get them in here and they just become factories for the most part. For the most part what I've seen, at least the ones that I've looked at and probably I'm always looking at, you know, the where the bad or the ugly spots are, but most of those are hate factories. I'm sorry. Most of those are hate factories."
"If there's one where they're truly teaching the, you know, the fundamentals of the Quran, OK." he continued. "But why, you know, maybe, but why is it that we still see the problems that we see?"
Christine Fair, an associate professor in the Security Studies Program at Georgetown University, said in an interview that she was not aware of one Muslim country in the Middle East or elsewhere that relied mostly on madrasas to educate its youth.
"The data on this is really quite variable," she said. "But it really does appear to be a very small number of people who only attend a madrasas."
Though madrasas promote varying interpretations of the Islamic faith, their main role as educational institutions is to teach the memorization of the Koran.
Emails to Flynn and the Trump transition team were not returned.
Arguably the country that US analysts and policymakers most commonly cite as containing a concerning number of extremist madrasas is Pakistan, which Flynn may not have meant to include, since it is not in the Middle East. Even there, however, Flynn's estimate about the role of madrasas in the education system would be vastly overstated. In a 2015 paper on madrasas in Pakistan, Fair found that they accounted for about 5% of all educational institutions in the country and "about 1% of full-time educational enrollments."
Madrasas have long been targets of criticism for those who, like Flynn, consider them hubs of radical interpretations of Islam. The 9/11 Commission described the religious schools "incubators of violent extremism." Colin Powell once called them breeding grounds for "for fundamentalists and terrorists."
While those who have studied the issue acknowledge that some madrasas do teach an extremist ideology and can foster sectarianism among students, they say that the link between madrasas and terrorism is also much less clear than Flynn suggests.
"I certainly recognize that some madrasas, especially in Pakistan, do promote radical and anti-Western interpretations of Islam," said Robert Hefner, who directs Boston University's program on Islam. "But across the broader Middle East, this is not just a minority -- it's a tiny minority."
"I haven't seen any reliable data that detect that religious educational institutions have produced a significant number of trans-national terrorists," said Ali Riaz, a professor at Illinois State University who has studied madrasas in South Asia. He noted that a large number of international terrorists have been highly educated, with some having attended engineering schools.
Statistics in a 2006 article in the Washington Quarterly by Peter Bergen, an author and CNN national security analyst, and Swati Pandey, bear this out. The article found that though all of the terrorists who plotted the World Trade Center bombing in 1993, the 1998 Africa embassy bombings, the 9/11 attacks, the 2002 Bali nightclub bombings, or the 2005 London attacks, had university degrees, none had attended a madrasa. Of the 79 terrorists responsible for those attacks, the article found that 11% had attended a madrasa.
Bergen told CNN's KFile that for international terrorists bent on entering the United States, a greater level of education is required.
"The kind of education you get in the average madrasa, if you enter an extremist one, it might make you a good foot soldier for the Taliban but it wouldn't get you past customs at JFK," he said.
According to Georgetown's Fair, while groups like the Taliban rely heavily on recruits from madrasas, groups like Al Qaeda do not.
Flynn, who was director of the Defense Intelligence Agency from 2012 to 2014, has come under criticism for his views on Islam during the campaign and after Trump announced that he would be the national security adviser for the incoming administration. The retired general tweeted in February that "Fear of Muslims is RATIONAL." The tweet was accompanied by a link to a video claiming Islamophobia was rational and that Islam wanted 80% of humanity enslaved or exterminated.
Riaz called Flynn's views on madrasas "deeply troubling," saying that policies based on them could risk isolating the US from Muslim countries in the battle against terrorism.
"By going back to this kind of policy, we isolate ourselves in this battle," he said.
Fair said that Flynn's focus on madrasas as a source of extremism calls into question his view of Iran as the "linchpin" of an anti-Western coalition that includes countries from North Korea to Russia. Where countries like Saudi Arabia, a US ally, sponsor madrasas around the world that promote an exclusionary view of Islam, "the one country in the region which is not doing this is actually Iran," she said.
"I found the comment to just bely an enormous amount of ignorance," she argued of Flynn's speech.