An online news site reported Wednesday that U.S. intelligence and law enforcement agencies monitored the e-mails of several prominent Muslim American activists and attorneys, prompting cries of protest from civil liberties advocates and a strong rebuttal from the government.

A lengthy article published on the Intercept stated that the National Security Agency and the FBI monitored the e-mails of five Muslim Americans under procedures meant to target foreign terrorists and spies.

The surveillance, according to the article, apparently was conducted under the Foreign Intelligence Surveillance Act, which requires the government to have probable cause to believe that the American targets are agents of foreign powers or terrorists and are or may be involved in committing a crime. The article said it was unclear whether warrants were obtained and what the justification for the targeting was.

The Intercept article said the five men denied any involvement in terrorism or espionage and that none advocated violent jihad or are known to have been implicated in a crime. It quoted some of them as saying they believed they had been targeted because they were of Muslim heritage.

The piece, which resulted from a three-month investigation, elicited charges that the government was conducting surveillance that violated people’s constitutional rights.

“Since 9/11, American Muslim communities have been fair game for law enforcement tactics of the sort that were used against African American civil rights groups in the 1960s and ’70s,” said Faiza Patel, co-director of the Liberty and National Security Program at the Brennan Center for Justice. “By targeting the leaders of these communities for secret full-scale monitoring, the FBI has taken this tactic to another level. How can any of us who work to advance justice for American Muslims feel free to do our work if we fear the government is watching our every step?”

The government rejected the allegation.

“It is entirely false that U.S. intelligence agencies conduct electronic surveillance of political, religious or activist figures solely because they disagree with public policies or criticize the government, or for exercising constitutional rights,” the Office of the Director of National Intelligence (ODNI) and the Justice Department said in a joint statement.

The article was based on documents leaked by former NSA contractor Edward Snowden, which included a spreadsheet listing thousands of e-mail addresses monitored between 2002 and 2008.

One 2005 training document also carried a disparaging reference to Muslims, listing a fake target whose name was “Mohammed Raghead.”

“The use of the term ‘Raghead’ in a tutorial for intelligence officers is sickening,” said Elizabeth Goitein, co-director with Patel of the Brennan Center program. The burden is now on the administration to explain and justify what looks very much like an abuse of the intelligence community’s surveillance powers.”

NSA spokeswoman Vanee M. Vines, without confirming the authenticity of the training document, said, “NSA has not and would not approve official training documents that include insulting or inflammatory language. Any use of racial or ethnic stereotypes, slurs, or other similar language by employees is both unacceptable and inconsistent with NSA policy and core values.”

The ODNI and Justice Department did not directly address the cases of the five men but took issue with the suggestion that the targeting was based on people’s political or religious views. “Unlike some other nations, the United States does not monitor anyone’s communications in order to suppress criticism or to put people at a disadvantage based on their ethnicity, race, gender, sexual orientation or religion,” the statement said.

With “limited exceptions,” as in an emergency, U.S. intelligence agencies must have a court order from the Foreign Intelligence Surveillance Court to target any U.S. citizen or lawful permanent resident for electronic surveillance, it said.

Civil liberties advocates told the Intercept that the secretive nature of the process makes it impossible to know what level of evidence is used to authorize surveillance and noted that no application or order for foreign intelligence surveillance has ever been publicly disclosed — even to a criminal defendant or his lawyer in cases where the government later brings charges based on the surveillance.

“No U.S. person can be the subject of surveillance based solely on First Amendment activities, such as staging public rallies, organizing campaigns, writing critical essays, or expressing personal beliefs,” the ODNI and Justice Department statement said. “On the other hand, a person who the court finds is an agent of a foreign power under this rigorous standard is not exempted just because of his or her occupation.”