Later, Gibbs said that President Obama ordered that Deputy Chief of Staff Messina conduct an internal review, which will take a couple of weeks to complete.
"The President will look at that review and take any appropriate steps after that," Gibbs said.
Although the shoot was authorized, the normal system of public notification broke down, multiple officials said.
Bloomberg said he was so furious he wasn't told about the photo op, that before he talked further to his own staff and agencies about the lack of notice to him, he wanted "to calm down."
"Poor judgment would have been a nice way to put it," Bloomberg said of the government flyover.
A New York City employee was disciplined for failing to pass on the FAA fly over information when it arrived on the employee's desk at City Hall.
According to city officials the employee was "reprimanded" and a "letter was placed in his file."
No information was immediately available on what if any discipline was meted out at the NYPD, where a second FAA notice was received last Thursday.
Eyewitnesses told ABCNews.com that they were "shocked" and "running scared" when the planes flew overhead.
Elena Zaccario, who works at an office building near Battery Park, said she was too startled to grab her camera until the planes' third fly-by.
"Needless to say, everyone was concerned and upset about not being notified like in previous 'military fly-overs,"" she said. "Other offices on other floors fled the building in panic. Not acceptable!"
Back Up Presidential Plane
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.