US authorities have been secretly monitoring radiation levels at Muslim sites amid fears that terrorists might obtain nuclear weapons, it has emerged.
The magazine says the targets were nearly all identified by the FBI
Scores of mosques and private addresses have been checked for radiation, the US News and World Report says.
A Justice Department spokesman said the programme was necessary in the fight against al-Qaeda.
Last week, President George W Bush admitted allowing the wiretapping of Americans with suspected terror links.
Mr Bush has defended the covert programme and vowed to continue the practice, saying it was vital to protect the country.
According to US News and World Report, the nuclear surveillance programme was set up after the attacks of 11 September 2001.
It began in early 2002 and has been run by the FBI and the Department of Energy's Nuclear Emergency Support Team.
The Associated Press news agency said federal law enforcement officials have confirmed the programme's existence.
The air monitoring targeted private US property in the Washington DC area, including Maryland and Virginia suburbs, and the cities of Chicago, Detroit, Las Vegas, New York and Seattle, the magazine said.
At its peak, three vehicles in Washington monitored 120 sites a day.
Nearly all of the targets were key Muslim sites.
"In numerous cases, the monitoring required investigators to go on to the property under surveillance, although no search warrants or court orders were ever obtained, according to those with knowledge of the programme," the publication said.
"The targets were almost all US citizens," an unnamed source involved in the programme told the magazine.
"A lot of us thought it was questionable, but people who complained nearly lost their jobs," the source said.
Federal officials cited by US News and World Report said that monitoring on public property, such as driveways and parking lots, was legal and that warrants were not needed for the kind of radiation sampling it conducted.
They also rejected the claim that the programme specifically targeted Muslims.
A spokesman for the Department of Justice said the programme was necessary as al-Qaeda remained committed to obtaining nuclear weapons.
An FBI spokesman declined to confirm or deny the report.
Ibrahim Hooper, spokesman for the Washington-based Council on American-Islamic Relations, said the news "comes as a complete shock to us and everyone in the Muslim community".
He added: "This creates the appearance that Muslims are targeted simply for being Muslims. I don't think this is the message the government wants to send at this time."