According to officials, the flight -- authorized by the FAA -- came in as low as 1000 feet to 150 feet above the city as it made a large circle over Manhattan, Staten Island, and New Jersey. The plane used was the back up presidential plane.
Self-evacuations of buildings in lower Manhattan and New Jersey, including the New York Mercantile Exchange, took place during the fly over.
According to multiple agencies, they were notified of the flyover last week, however the general public was not notified.
The Defense Department conducted the photo opportunity over the Hudson River. The planes flew over Lower Manhattan and in the vicinity of the Statue of Liberty during a 15 minute, pre-planned flight.
Local authorities were told not to disclose information about this morning's flyover, the New York City Police Department said in a statement.
"The flight of a VC-25 aircraft (the military version of the 747) 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," police said.
Other officials noted that they were led to believe the flight would be limited to the area near the Statue of Liberty, however the flight pattern was above a much larger portion of New York and at an extremely low altitude.
Dan Matlack, in Jersey City, NJ across from Manhattan, said people were running to get away, with flashbacks to 9-11.
The plane was "really close to the ground and banking hard and 'seemed' like it was heading for the Goldman Sachs building in [Jersey City] to us on the ground," Matlack told ABCNews.com.
New York Sen. Chuck Schumer said the flyover "borders on being cruel or very, very stupid."
After 9-11, he said, 'If you're going to see large jets flying low over New York City, people are going to panic."
Megan Chuchmach and Jake Tapper contributed to this report.