President Barack Obama called the attack in the heart of a military complex a "cowardly act."
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One shooter had been killed, but police were looking for two other potential gunmen wearing military-style uniforms, District of Columbia Police Chief Cathy Lanier said.
Authorities identified the dead shooter as a Navy employee Aaron Alexis, whose work status had been changed earlier this year, said a federal government official who spoke only on condition of anonymity. While that may suggest the motive was job related, authorities haven't ruled out anything including terrorism, the official said.
The rampage led to tightened security at the Capitol nearby.
Witnesses described a gunman firing down on a cafeteria from an upper floor and a gunman firing at people in a hallway on another floor.
Two Navy officials say at least six people were killed in the rampage. DC Mayor Vincent Gray said four people were wounded and taken to hospitals.
About 3,000 people work at the Naval Sea Systems Command headquarters, which builds, buys and maintains the Navy's ships and submarines and combat systems.
Todd Brundidge said he and other co-workers encountered a gunman in a hallway on the third floor. The gunman was wearing all blue, he said.
"He just turned and started firing," Brundidge said.
Terrie Durham said she also saw the gunman.
"He aimed high and missed," she said. "He said nothing. As soon as I realized he was shooting, we just said, 'Get out of the building.'"
Rick Mason said a gunman was shooting from a fourth-floor overlook in the hallway outside his office. He said the gunman was aiming down at people in the building's cafeteria. Mason said he could hear the shots but could not see a gunman.
Shortly after the gunfire, Mason said someone on an overhead speaker told workers to seek shelter and later to head for the gates at the complex.
Patricia Ward said she was in the cafeteria.
"It was three gunshots straight in a row - pop, pop, pop. Three seconds later, it was pop, pop, pop, pop, pop, so it was like about a total of seven gunshots, and we just started running," Ward told reporters.
Ward said security officers started directing people out of the building with guns drawn.
Janis Orlowski, chief operating officer of Washington Hospital Center, told reporters the hospital was treating three gunshot victims in critical condition.
A US Park Police helicopter hovered over the Navy building and appeared to drop a basket with a person onto the roof.
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