Training presentations for US security forces, obtained by Wired.com, describe mainstream Muslims as terrorist sympathisers, call the Prophet Muhammad a "cult leader" and state that more "devout" Muslims, are more likely to be "violent".
The FBI has said it no longer uses the manual, but one civil rights group compares providing information for security forces, written by "Islamophobes", to "asking the Klu Klux Klan to train agents on racial sensibility".
"The training material is garbage written by hate groups," said Abed Ayoub, a lawyer and campaigner with the American-Arab Anti-Discrimination Committee.
"The individuals who wrote this material are hate mongers. We would not allow this to happen to other groups in our society," he told Al Jazeera.
The presentations were used by the FBI in Quantico, Virginia, teaching agents that the Islamic practice of giving charity is nothing more than a mechanism for funding combat.
A section in the training presentations titled "just War" principles of Islam states that Muslims believe "War is the rule and peace is only temporary", while another claims there can be no peace between Islam and other faiths until "Islam conquers and assimilates its adversary".
Spencer Ackerman, the journalist who broke this story for Wired, told Al Jazeera that: "There is still a real ignorance and to some degree a real fear of Islam that has found a surprising home in the FBI."
A federal law enforcement official, speaking to the AP news agency on the condition of anonymity, said the lecture was given for just three days last April.
"The larger question is: How did this material get used in the first place?" Ayoub wondered. "And what safeguards will the FBI put in place to make sure it doesn't happen again?"
The leaked training documents confirm fears that some Muslim leaders have had about law enforcement since the 9/11 attacks.
"Unfortunately, we have been asking government officials to address anti-Islam training for some time," Ibrahim Hooper, spokesperson for the Council on American-Islamic Relations, told Al Jazeera.
"This is finally coming to light and will hopefully lead to reforms and scrutiny of those training our nation's security personnel."
Previous FBI training material from 2009, also obtained by Wired, shows that Robert Spencer's book The Truth about Mohammed: Founder of the World’s Most Intolerant Religion was considered recommended reading material.
Spencer has been one of the ringleaders of protests against the so-called “Ground Zero Mosque” in New York.
His anti-Islam writings were frequently cited in a manifesto written by Andres Behring Breivik who launched attacks in Norway, killing 77 people at a youth camp.
"The FBI really had to scrape the bottom of the barrel to recommend Spencer," Hooper said.
"I think there are competing factions in the FBI. One wants to view all Muslims with suspicion and the other faction views this – rightly – as counter-productive to our nation’s security."
Islamic leaders believe the vilification in this type of training has led to increased harassment and profiling of Muslim communities in the US.
"In the past year we have seen complaints about agent provocateurs being sent to mosques, data mapping of our communities and unconstitutional surveillance," Ayoub said.
"These actions undermine our efforts and the constructive dialogue we are trying to maintain in moving forward.
"Ten years after 9/11, the community is tired of being lied to and given false promises. We need to be working together [with law enforcement] and not against each other. It looks like they are working against us from actions like this."
If he were asked to host training sessions for the FBI, Ayoub said he would start from a simple premise: "Arab and Muslim American communities are just like everyone else."
The most alarming revelation from the manual for Ayoub is the equation of religious devotion and propensity to violence. "That is the first thing which needs to be cleaned up," he said.
Along with being bigoted, the link between religious devotion and terrorism will not help stop attacks, Spencer Ackerman said.
"If they [FBI agents] spend their time and resources going after indicators of violent behaviour based on the amount of religiosity a person displays, then first of all they are not going to get actual terrorists, but innocent people."