WASHINGTON — An online magazine reported Wednesday that the National Security Agency and the FBI covertly scanned the emails of five prominent Muslim-Americans under the government’s secret surveillance program aimed at foreign terrorists and other national security threats.

The report in The Intercept, a venture by journalist Glenn Greenwald, said the targets included an attorney, a Republican political operative, a university professor and two civil rights activists. The Intercept said all five denied any involvement in terrorism or espionage and had not been accused of any crimes. The magazine questioned whether the government obtained legal permission for its surveillance.

The Intercept account said its investigation using classified documents obtained from former NSA contract systems analyst Edward Snowden showed that “the system for authorizing NSA surveillance affords the government wide latitude in spying on U.S. citizens.” The article also said that some government training materials included a slur against Muslims.

NSA and Justice Department officials denied Wednesday that American activists are targeted for criticizing the government. Americans are only targeted for email surveillance if there is probable cause, they said.