Assistant Director John Miller said in a statement that the agency "does not target any group based on ethnicity, political or religious belief."
An unnamed federal official told the New York Times that monitoring was done in places that seemed likely terrorist targets.
"If you can go drive a car into the parking lot near the shopping mall, we can go there," he said.
A report this week on the U.S. News & World Report Web site said that the FBI monitored a number of private U.S. sites for radioactivity in the last three years, many of them mosques, homes or businesses of Muslims.
The Times said the government has acknowledged the radioactivity monitoring at ports, subway stations and other public places, but the monitoring of private property was not generally known.
The monitoring involves the use of small radiation alarms, worn like pagers on the belt.
Much of the private site monitoring took place in Washington, New York, Chicago, Detroit, Las Vegas and Seattle, reports said. Since the agents were monitoring from public areas, no warrants were sought.
U.S. officials have been concerned terrorists might use a "dirty bomb," a conventional explosive device wrapped in radioactive material, inside the United States.
None of the reports suggested the monitoring uncovered any radiation.