But the flyover was nothing but a photo op, apparently one of a series of flights to get pictures of the plane in front of national landmarks.
The exercise involved an F-16 escorting the plane, a Boeing 747, over Battery Park City and up the Hudson River. Some reports quoted an administration official who said the purpose of the photo op was to update file photos of the president's plane near the Lady Liberty.
The large plane is the military version of the 747 and is the type of plane the president uses to fly. When he is aboard, the plane is referred to as Air Force One.
The head of White House Military Office apologized for the incident late Monday.
"Last week, I approved a mission over New York. I take responsibility for that decision," said Louis Caledra. "While federal authorities took the proper steps to notify state and local authorities in New York and New Jersey, it's clear that the mission created confusion and disruption. I apologize and take responsibility for any distress that flight caused."
President Obama was apparently not informed of the flight. When he learned what happened, sources said Obama was furious.
The maneuver was coordinated in advance with the FAA and state and local officials.
The Defense Department "coordinated the flight with FAA," FAA spokeman Jim Peters said, "and we made the notifications to the city of New York, as well as the 311 and 911 centers, the NYPD, New Jersey State Police and various operations centers in the New York area."
City officials were notified, but not the general public.
"The flight of a VC-25 aircraft and F-16 fighters this morning was authorized by the FAA for the vicinity of the Statue of Liberty with directives to local authorities not to disclose information about it, but to direct any inquiries to the FAA Air Traffic Security Coordinator," a police statement read.
New York City Mayor Michael Bloomberg says he is furious that the federal government flew the planes near Ground Zero. Bloomberg says the flyover so near the World Trade Center site showed "poor judgment" and was insensitive. He says he is furious that the NYPD and another city agency were notified last week, but did not tell him.
If he had known, Bloomberg says he would have tried to stop it.
NEW YORK AND TRI-STATE AREA NEWS