Sources told the Los Angeles Times the pilot had been arrested, Secret Service agents had interviewed him and the incident appears to have been unintentional.
It was uncertain whether the pilot, who was not identified, would face any criminal charges.
Two F-16 military fighter jets intercepted the Piper 28 aircraft and guided it to El Monte Airport.
Obama arrived at Los Angeles International Airport from the west Los Angeles community of Cheviot Hills by helicopter, then left the airport at 9:53 a.m. on Air Force One.
Much of Los Angeles' airspace was under flight restrictions because of the president's trip.
In February, another small plane was intercepted after entering Los Angeles airspace closed because of a presidential visit.
Police said the pilot of that plane, a Cessna four-seater, was arrested after he landed in Long Beach, the Times reported at the time.
The newspaper said Friday as much as 10 kilograms of marijuana that was aboard the plane was seized.