The "dirtbox" devices mimic mobile phone tower transmissions, and handsets transmit back their location and unique identity data, the report claims.
While they are used to track specific suspects, all mobile devices in the area will respond to the signal.
The US Justice Department refused to confirm or deny the report.
The Wall Street Journal said it had spoken to "sources familiar with the programme" who said Cessna aircraft fitted with dirtboxes were flying from at least five US airports.
The department said that it operated within federal law.
A dirtbox mimics the signals transmitted by mobile phone providers which handsets look to latch on to. When they do, they send their individual registration information and location.