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It was supposed to be a photo opportunity, a showcase of Air Force One alongside the sweep of New York City skyline.

But as the low-flying Boeing 747 speeded in the shadows of skyscrapers, trailed by two fighter jets, the sight instead awakened barely dormant fears of a terrorist attack, causing a momentary panic that sent workers pouring out of office buildings on both sides of the Hudson River.

“I thought there was some kind of an attack,” said Paul Nadler, who sprinted down more than 20 flights of stairs after watching the plane from his office building in Jersey City shortly after 10 a.m. “We ran like hell.”

In fact, the blue-and-white plane with “The United States of America” emblazoned on its side was one of two regularly used by the president. It was soaring above Lower Manhattan, Staten Island and Jersey City so government photographers could take publicity pictures near the Statue of Liberty.

Aides to President Barack Obama, who was not on board, said he was incensed when he learned of the event Monday afternoon. The White House later issued a formal apology.

Witnesses described the engine roar as the planes swooped by office towers close enough to rattle the windows and prompt evacuations at scores of buildings. Some sobbed as they made their way to the street.

“As soon as someone saw how close it got to the buildings, people literally ran out,” said Carlina Rivera, 25, who works at an educational services company on the 22nd floor of 1 Liberty Plaza, adjacent to the site of the Sept. 11, 2001, attack. “Probably about 80 percent of my office left within two minutes of seeing how close it got to our building.”

Under federal regulations, in urban areas, airplanes must fly at least 1,000 feet above obstructions like buildings and bridges, and jetliner flights over Manhattan are typically at 8,000 feet or more. And planes do not typically approach local airports by flying low over the harbor.

As the fright wore off, Mayor Michael R. Bloomberg and other local leaders questioned why the Federal Aviation Administration had ordered local officials, including the New York Police Department, not to alert the public in advance.

An FAA memo last week said information about the exercise “should only be shared with persons with a need to know” and “shall not be released to the public or the media.”

The breakdown of communication went deeper. Bloomberg said he first learned of the exercise when his BlackBerry started buzzing with messages from people asking if he knew what was going on.

“First thing is, I’m annoyed — furious is a better word — that I wasn’t told,” Bloomberg said.

“Why the Defense Department wanted to do a photo-op right around the site of the World Trade Center catastrophe defies imagination,” he said. “Had I known about it, I would have called them right away and asked them not to.”