The FBI has been sending surveillance planes over a number of major cities in the US.
The planes were operated under fictitious aviation companies.
The low-flying aircraft have video cameras on board and advanced technology which can identify people with mobile phones and detect phone records even though they are thousands of feet below and in their own homes.
The revelation was made by an Associated Press investigation which found that the FBI had at least 13 fake firms to register the light aircraft, usually small Cessnas.
More than 100 flights appear to have been made in the last month covering major cities such as Boston, Seattle and Houston.
According to the FBI, the aircraft are "not equipped, designed or used for bulk collection activities or mass surveillance". An FBI spokesperson said the technology was rarely used but it does let the government pinpoint the whereabouts of people who are not under suspicion but just happen to be near the surveillance aircraft flight path.
The programme was first rumbled in May when a plane was seen circling above a Baltimore crowd protesting the death of a young black man who died in police custody. The flight was tracked back to the FBI.
The disclosure comes as the US Senate debates a bill which would stop the country’s National Security Administration from collecting the phone records of Americans.
A standoff by Republicans meant that the Patriot Act lapsed on Sunday with no replacement for it.
