The Federal Aviation Administration (FAA) said he was piloting a small plane that wrongly crossed a runway where another aircraft was landing.
The planes were within about 3,600ft (1,100m) of each other at Los Angeles' Hawthorne airport last Friday. There was no danger of a crash, the FAA said.
Ford, 77, acknowledged his mistake and apologised, his representative said.
The representative said in a statement that the star of the Indiana Jones and Star Wars films had "misheard" an instruction from air traffic control.
"The purpose of the flight was to maintain currency and proficiency in the aircraft. No one was injured and there was never any danger of a collision," the statement said.
Ford was at the controls of a two-seat Aviat Husky light plane.
It is not the first time Ford, a well-known aviation enthusiast, has been involved in air accidents.
Ford took up flying when he was in his 50s and is also trained to fly helicopters.
In 1999, he crash-landed his helicopter during a training flight in Los Angeles but both he and the instructor were unhurt.
A year later a plane he was flying had to make an emergency landing in Nebraska. Again he and his passenger escaped unhurt.