Police discovered about 40 pounds of marijuana inside the plane after it landed at Long Beach Airport, a law enforcement official said. The official was not authorized to comment publicly on the drug investigation and spoke under condition of anonymity.
The Secret Service said the president was never in any danger.
In a statement, the North American Aerospace Defense Command said it scrambled two F-16 fighters from March Air Reserve Base in Riverside County, Calif., to intercept a Cessna 182 over Los Angeles about 2:30 p.m. EST.
U.S. Immigration and Customs Enforcement spokeswoman Virginia Kice said the department's Homeland Security Investigations unit questioned the pilot, who has been turned over to Long Beach police and remains in custody. He will face local prosecution, Kice said.
NORAD spokesman Michael Kucharek declined to disclose how close the Cessna came to Marine One.
The Federal Aviation Administration had notified pilots that there was an eight-mile radius around Los Angeles International Airport that was off-limits to air traffic Thursday, spokeswoman Brie Sachse said. It was that radius that the Cessna violated.
Sachse declined to release the Cessna's tail number, saying the agency doesn't identify planes involved in security incidents.
