War planes were seen flying overhead and security cars rushed away from the buildings.
A senior law enforcement official said the alarm was caused by an aircraft intruding into the protected airspace over Washington.
Workers were allowed to return to the buildings within minutes of the false alarm being realised.
Sarah Little, an aide to Senator Pat Roberts, said the order to evacuate came over the special pager devices that every congressional office has.
“They said to head south because there is an imminent aircraft threat,” Ms Little said.
Reporters in the White House were told to move to a more secure location.
A guard in the West Wing of the White House shouted at reporters, “Go down into the basement.”
“Leave, run,” security officers shouted to staff and reporters at the Capitol building.
“This is not a drill,” guards shouted as they moved people away from the building.
Congressional leaders were moved from the Capitol building.
President George W Bush was away from the White House exercising on his bicycle at the time.
Shortly after noon (5pm Irish time) officers rushed through the Supreme Court building and told staff to get into the basement.
At the Treasury Department, people were moved across the street.
Several other government buildings ordered people to safer locations.
The plane was approached by a fighter aircraft and veered away.
A Federal Aviation Administration official said the plane was a Cessna.
The security breach prompted alerts across the city.
The capital, which was targeted on September 11, 2001 has been under a heightened state of alert since then.
The evacuation was the most urgent since President Ronald Reagan’s funeral last June, when officials lost track of an arriving plane carrying Kentucky Governor Ernie Fletcher little more than an hour before Reagan’s casket was to arrive at the Capitol building to lie in state.
Following Mr Bush’s visit to Georgia on Tuesday, it was yesterday revealed an inactive grenade had been found near the site where Mr Bush made a speech in Tbilisi.
Gela Bezhuashvili, secretary of the National Security Council, said the Soviet-made grenade was found 100 feet from where Bush spoke.
Reports yesterday said it had been thrown at the stage where Mr Bush was, however the security chief said it had not been thrown.
“The goal is clear - to frighten or to scare people and to attract the attention of the mass media,” he said.
“The goal has been reached and that is why I’m talking to you now.
“In any case there was no danger whatsoever for the president,” he said.