Authorities said they were looking for a possible second attacker who may have been disguised in an olive-drab military-style uniform.
But as the day wore on and night fell, the rampage increasingly appeared to be the work of a lone gunman, and Navy Yard employees were being released from the complex and children were let out of their locked-down schools.
Investigators said they had not established a motive for the rampage, which unfolded about 8:20 a.m. in the heart of the nation's capital, less than four miles from the White House and two miles from the Capitol.
As for whether it may have been a terrorist attack, Mayor Vincent Gray said: "We don't have any reason to think that at this stage." But he said the possibility had not been ruled out.
It was the deadliest shooting rampage at a U.S.-based military installation since Maj. Nidal Hasan killed 13 people and wounded more than 30 others in 2009 at Fort Hood in Texas. He was convicted last month and sentenced to death.
President Barack Obama lamented yet another mass shooting in the U.S. that he said took the lives of American patriots. He promised to make sure "whoever carried out this cowardly act is held responsible."
The FBI took charge of the investigation and identified the gunman killed in the attack as 34-year-old Aaron Alexis of Texas. He died after a running gunbattle with police, investigators said.
A federal law enforcement official who was not authorized to discuss the case publicly and spoke on condition of anonymity said Alexis was believed to have gotten into the Navy Yard by using someone else's identification card. But Navy officials said it was not yet clear how he got onto the base.
Alexis was a full-time reservist from 2007 to early 2011, leaving as a petty officer third class, the Navy said. It did not say why he left. He had been working for a fleet logistics support squadron in Fort Worth, Texas. The Navy listed his home of record as New York City.
At the time of the rampage, he was working as a Defense Department contractor, but it was not clear if the information technology worker was assigned at the Naval Yard, according to two defense officials who spoke on condition of anonymity because they were not authorized to discuss the matter publicly.
He was also pursuing a bachelor's degree in aeronautics online with Embry-Riddle Aeronautical University, the school said. He started classes in July 2012.
In addition to those killed, more than a dozen people were hurt, including a police officer and two female civilians who were shot and wounded. They were all expected to survive.
The Washington Navy Yard is a sprawling labyrinth of buildings and streets protected by armed guards and metal detectors, and employees have to show their IDs at doors and gates to come and go. About 20,000 people work there.
The rampage took place at Building 197, the headquarters for Naval Sea Systems Command, which buys, builds and maintains ships, submarines and combat systems. About 3,000 people work at headquarters, many of them civilians.
Witnesses described a gunman opening fire from a fourth-floor overlook, aiming down on people in the cafeteria on the main floor. Others said a gunman fired at them in a third-floor hallway.
Patricia Ward, a logistics-management specialist, said she was in the cafeteria getting breakfast.
"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 said.
Todd Brundidge, an executive assistant with Navy Sea Systems Command, said he and other co-workers encountered a gunman in a long hallway on the third floor. The gunman was wearing all blue, he said.
"He just turned and started firing," Brundidge said.
Terrie Durham, an executive assistant with the same agency, said the gunman firing toward her and Brundidge.
"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.'"
Police would not give any details on the gunman's weaponry, but witnesses said the man they saw had a long gun — which can mean a rifle or a shotgun.
In the confusion, police said around midday that they were searching for two men who may have taken part in the attack — one carrying a handgun and wearing a tan Navy-style uniform and a beret, the other armed with a long gun and wearing an olive-green uniform. Washington Police Chief Cathy Lanier said it was unclear if the men were members of the military.
But later in the day, police said the man in the tan uniform had been identified and was not involved in the shooting.
As emergency vehicles and law enforcement officers flooded streets around the complex, a helicopter hovered, nearby schools were locked down and airplanes at nearby Reagan National Airport were grounded so they would not interfere with law-enforcement choppers.
Security was tightened at other federal buildings. Senate officials shut down their side of the Capitol while authorities searched for the potential second attacker. The House remained open.
Adm. Jonathan Greenert, chief of naval operations, was at the base at the time the shooting began but was moved unharmed to a nearby military installation.
Anxious relatives and friends of those who work at the complex waited to hear from loved ones.
Tech Sgt. David Reyes, who works at Andrews Air Force Base, said he was waiting to pick up his wife, Dina, who was under lockdown in a building next to where the shooting happened. She sent him a text message.
"They are under lockdown because they just don't know," Reyes said. "They have to check every building in there, and they have to check every room and just, of course, a lot of rooms and a lot of buildings."
According to public records, Alexis' neighbor called Fort Worth police in September 2010 after she was nearly struck by a bullet that came from his downstairs apartment. Alexis told police he was cleaning his gun when it went off.
He was arrested on suspicion of discharging a firearm within city limits but was not prosecuted.