Louis Caldera, the man who approved the low-flying Air Force One plane that panicked New York City, delivered his resignation Friday as the White House released a photo of the plane flying over Ellis Island.

President Obama has accepted the resignation, White House Press Secretary Robert Gibbs said in a statement. 

Caldera apologized the day after the April 27 incident that sent New Yorkers out into the streets as the 747 followed by two F-16s flew low over the Manhattan skyline.

In his resignation letter, the former Army secretary said that he has concluded that the controversy surrounding the photo shoot "has made it impossible for me to effectively lead the White House Military Office."

"Moreover, it has become a distraction to the important work you are doing as president. After much reflection, I believe it is incumbent on me to tender my resignation and step down as director of the White House Military Office," he wrote. 

Caldera's resignation is effective May 22, though he will spend the next two weeks not directing the office, but completing the "necessary out-processing."

Click here to read the resignation letter (.pdf).

Gibbs said that Obama has asked Jim Messina, his deputy chief of staff, and Defense Secretary Robert Gates or his designee "to jointly review the organizational structure of the White House Military Office and the reporting relationship of its components to the White House and the Air Force, and to make recommendations to him to ensure that such an incident never occurs again.

An internal review of the incident conducted by the White House found that on April 3, participants of a teleconference between the Presidential Airlift Group, the Federal Aviation Administration and local officials discussed the date, time, location, altitude and flight path for the plane.

"The participants recognized 'the sensitivity of the aircraft involved,' and conclude' that 'public affairs and outreach efforts must be carefully coordinated and timed,'" according to the review. "Coordination with 'the general public' was planned to commence two days before flight.'"

Click here to read the White House internal review of the flyover incident.

The report indicated that Caldera did not notify the appropriate people within the White House, including deputy White House Chief of Staff Jim Messina or White House spokesman Robert Gibbs about the flyover. When asked why he didn't, Caldera suggested it may have been an oversight, the report said.

Caldera said his deputy did not tell him and didn't understand that the presidential jet would be flying over lower Manhattan, the report said, and that he was not asked to approve the flight.

Gates did not participate in the planning of the flyover. He has ordered a review of notification procedures for high-visibility "training events." 

In a letter responding to a request by Sen. John McCain, the ranking Republican on the Senate Armed Services Committee, Gates wrote that he was concerned that the public had not been adequately informed about the flyover. 

"I am concerned that this highly public and visible mission did not include an appropriate public affairs plan nor adequate review and approval by senior Air Force and (Department of Defense) officials," Gates wrote in the letter dated Tuesday and later obtained by FOX News. 

Participants on the flight included one combat photographer, a standard crew complement for Air Force One and the two F-16s that accompanied it and no non-duty personnel or extra passengers, Gates wrote.  

Gates wrote the mission was planned in late March 2009 and was coordinated by the White House Military Office's Presidential Airlift Unit, which is an Air Force unit; Federal Aviation Administration liaisons; a Systems Operations Security team; traffic managers; New York air traffic control representatives and Newark and LaGuardia tower supervisors. 

Gates wrote the FAA notified several agencies on April 24, 2009, about the impending event, including the U.S. Park Police, the New York City mayor's office, the New York City Office of Emergency Management, New York City Police Department Operations, New Jersey State Police Regional Coordination Center and New Jersey area emergency operations centers in Newark, Jersey City, Bayonne, Hoboken and Elizabeth.

The plane flew at FAA-approved altitude, according to the defense secretary. In conjunction with the photo shoot, the pilots also practiced instrument approaches and landings at Atlantic City International Airport, an approved training location.

The April 27 flyover sparked chaos in the city since the public, and even Mayor Michael Bloomberg, had not been notified it would take place. Thousands of New Yorkers, reminded of the Sept. 11, 2001, terrorist attacks, quickly evacuated office buildings and emergency call centers were inundated. 

"The reaction to the low-flying VC-25 and F-16 fighter aircraft over New York City (NYC) is understandable, and we deeply regret the anxiety and alarm that resulted from this mission," Gates wrote.

A day after the flight, President Obama denounced the photo-op, which cost $328,835, calling it "a mistake." 

Earlier this week, the Obama administration did an about-face when it first announced it would not release any pictures of the flyover even though officials said the whole reason for it was to take publicity photos and give pilots some flying time. The next day Press Secretary Robert Gibbs said a photo would be forthcoming.

Gates wrote that he was also concerned that an Air National Guard aircraft was used in the mission. 

"I have asked the chairman of the Joint Chiefs of Staff to ensure that the Military Service and National Guard Bureau procedures for such activities include appropriate safeguards, checks and balances to ensure missions of this type are properly reviewed, vetted and announced in the future," he wrote.