The CIA and the US Marshals Service of Department of Justice has developed this technology in what The Wall Street Journal called "a high-tech hunt for criminal suspects".
But those gadgets, known to law enforcement officials as "dirtboxes," also scoop up data from tens of thousands of unsuspecting mobile users, the paper's unnamed sources said.
The programme operates specially equipped planes that fly from five US cities, with a flying range covering most of the US population, it said.
The surveillance system briefly identifies large numbers of cellphones belonging to citizens unrelated to the search.
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The practice can also briefly interfere with the ability to make calls, these people said, according to the daily.
According to a CIA spokesman quoted in the news report, some technologies developed by the agency have been lawfully and responsibly shared with other US government agencies.
"How those agencies use that technology is determined by the legal authorities that govern the operations of those individual organizations-not CIA," the CIA Spokesman said.
The agency doesn't conduct "domestic surveillance, intelligence gathering, or any type of bulk data collection," the spokesman said, adding that it doesn't gather any intelligence on behalf of US spy agencies.
Electronic Frontier Foundation has filed a lawsuit seeking more details about the programme and its origins.
"There's a lot of privacy concerns in something this widespread, and those concerns only increase if we have an intelligence agency coordinating with them," Crocker of the Electronic Frontier Foundation told the daily.