The blushes of US officials over the low-flying passage of a 747 jet above downtown Manhattan on Monday have turned a deeper shade of red after it was that the authorities informed New York in advance but ordered the details to be kept secret from the public.

The flyover of a member of the president's Air Force One fleet, accompanied by two fighter jets, prompted mass panic on the streets among hundreds of New Yorkers who feared a repeat of 9/11. Many downtown offices were vacated, and the emergency services flooded with distress calls.

The stunt, costing $328,835 of taxpayers' money, was designed as a publicity photo shoot to get a picture of the presidential plane with the Statue of Liberty in the background. But it backfired, forcing President Obama to apologise.

"It was a mistake, as was stated ... and it will not happen again," Obama said. He has let his anger over the incident be known, and has ordered a probe into what happened.

It now transpires that the Federal Aviation Administration, in charge of the project, did inform key agencies ahead of the flyover, in full awareness of the possibility that low-flying planes could provoke unease among New Yorkers in the wake of 9/11. The New York police, the FBI and the Secret Service that protects the president were all told, but were ordered to keep the event secret even to the extent of federal sanctions being imposed if the news leaked.

The mayor's office was also informed, though in that case there were blushes for other reasons. The manager who was informed by the aviation administration forgot to pass it up the line to Mayor Bloomberg, and was reprimanded.

"I think we've all learned something from it and now it's time to make sure our procedures are better and to get on with other things," Bloomberg said.

"It does seem like it was a waste of money, but that's up to the federal government."