Police identified the alleged shooter as 34-year-old Aaron Alexis, of Forth Worth, Texas, who served full-time in the Navy from 2007 to 2011, the the FBI and Pentagon said.
The FBI appealed to the public for information on the suspect, who reportedly had once been arrested but not charged in Texas for shooting a bullet through his apartment ceiling.
"No piece of information is too small. We are looking to learn everything we can about his recent movements, his contacts and his associates," said Valerie Parlave, assistant director of the FBI's Washington field office.
The FBI released a photo of Alexis, an African-American who held the rank of an Aviation Electrician's Mate 3rd Class and had served full-time in a logistics support squadron in Forth Worth, according to the Navy.
The shooting sparked a massive show of force as police and federal agents surrounded the Navy Yard, cordoning off streets only blocks from the US Capitol, home of Congress.
Officials gave no indication of any link to terrorism but said the motive for the attack on the installation was unknown.
Washington DC Mayor Vincent Gray said "we don't have any reason at this stage to suspect terrorism, but certainly it has not been ruled out."
He announced the number of dead from the shooting spree was at 13, with about dozen more wounded, including a police officer.
Police said a second suspect was still being sought, an African-American male aged 40 to 50, clad in an olive-drab military-style uniform. And a possible third suspect was later cleared.
Earlier media reports had said the shooter was armed with an assault rifle and had allegedly barricaded himself in a room in a headquarters building.
After the first reports of shots came at 8:20 am (1320 GMT) in the headquarters building of the Naval Sea Systems Command, police arrived within three minutes and exchanged fire in "multiple engagements" with the suspect, police chief Cathy Lanier said.
It was unclear how the attacker could have penetrated the heavy security that surrounds the Navy Yard, which is located on the Anacostia River, less than two miles (three kilometers) from the Capitol.
Details on the suspect's background in the Navy raised the possibility that the shooter had a pass or identity card that could gain him entry to the facility, which includes an office that oversees ship-building programs and other buildings.
A Washington DC police officer was among those injured in the rampage, and hospital officials said he suffered serious wounds to his legs but was expected to survive.
One employee at the Navy Yard, Patricia Ward, said she had just paid for her breakfast at a cafeteria when shots rang out.
"I was waiting for my friend to pay when we heard the gun shot. It was three gun shots straight in a row, 'pow-pow-pow,'" she told reporters.
"Three seconds later it was 'pow-pow-pow.' So it was like a total of seven gun shots. And we just started running."
The guard "told all of us to just run, to get away as fast as you can."
She said employees do not have to pass through a metal detector when they enter the building.
Police earlier blocked off intersections around the Navy Yard as military troops in uniform stood guard at street corners and patrol boats moved in near the site along the banks of the Anacostia river.
Crowds of onlookers stood on sidewalks watching the drama unfold, as helicopters swarmed overhead.
Flights out of the nearby Reagan National Airport were briefly delayed and schools were on lockdown until anxious parents came to pick up their children in the afternoon.
The US Senate adjourned for the day as a precaution and Washington's baseball team, the Nationals, whose stadium is adjacent to the Navy Yard, called off its Monday evening game.
About 3,000 people work at the headquarters, which oversees the building and buying of warships and combat systems. The site, which includes a naval history museum, dates back to the early 1800s.
The complex also has a residence which serves as the home of the four-star chief of the US Navy, Admiral Jonathan Greenert.
President Barack Obama called the shooting a "cowardly act" and lamented that America was confronting "yet another mass shooting," saying troops in the military should not have to confront danger at home. (AFP)
