The White House went into lockdown, and both Obama and Vice President Joe Biden were "briefly relocated out of an abundance of caution", said White House spokesman Robert Gibbs.
On Capitol Hill, the US Senate adjourned into a quick recess but returned to session minutes later after the all-clear.
Gibbs did not refer to the measures as an evacuation, and the violation was so brief that people resumed their activities almost immediately.
MSNBC television reported that the pilot complied with demands to alter course. The all-clear signal was given just minutes later.
People at the White House's north lawn were told to get inside by the Secret Service. Gibbs did not comment on how Obama's family may have been affected by the alarm.
Extra precautions to protect the airspace around Washington were enacted following the Sep 11, 2001, terrorist attacks, when hijacked airplanes crashed into the Pentagon, the World Trade towers in New York City and a field in Pennsylvania.
- DPA
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