Valerie Parlave, assistant FBI director in charge of the Washington Field Office, identified the dead gunman as Aaron Alexis, 34, of Fort Worth. It was unclear whether Alexis acted alone.
The shooting began about 8:20 a.m. EDT and Metropolitan Police Chief Cathy Lanier told a 4 p.m. news conference the investigation was still active and it would be several hours before investigators determined whether any suspects were still at large.
Lanier repeated her comments at a 6 p.m. news conference, asking people in the area to stay away and shelter in place until the all clear is given. She said traffic closures across M Street were likely to stay in place throughout the night.
Lanier said officers were on the scene within minutes of the first call and engaged the shooter.
Mayor Vincent Gray said at least 13 people had been killed and a dozen more had been injured. He said there was no known motive for the shooting and authorities were still seeking the identity of a second suspect believed to be about 50 years of age and wearing a olive drab uniform.
Investigators were still in the process of identifying victims and notifying next of kin, Gray said.
"Though we do not have any further detail to share at this time about the deceased shooter, we again ask the public to look at the photos of Aaron Alexis and contact the FBI with any and all information," Parlave said at the 6 p.m. news conference, adding the investigation was "still very active."
The U.S. Senate placed itself on lockdown.
As many as three gunmen were initially thought to have been involved in the rampage and police spent much of the day searching for two other possible assailants inside the headquarters for Naval Sea Systems Command.
Late Monday afternoon, police said one of the two possible suspects -- a white male wearing a Navy-style khaki military uniform with a beret -- had been identified and was not considered a suspect or person of interest.
The Police Department was asking anyone with information to call (800) 225-5321.
Parlave said the FBI was seeking as much information as possible on Alexis, who some media outlets identified as a military contractor.
"No piece of information is too small," she said, adding the FBI wants to know about his recent movements and contacts. A picture of the suspect was posted in the FBI's website. Parlave said anyone with information on Alexis should call (800) 225-5324.
A Washington police officer and a base security guard were among the injured. The police officer and two civilian victims were taken to MedStar Washington Hospital Center. Chief Medical Officer Janis Orlowski said the injured police officer was treated for gunshot wounds to the leg. A female civilian was being treated for a gunshot wound to her shoulder and another woman, also a civilian, had gunshot wounds to her head and hand. All three were expected to survive, Orlowski said.
A man in his 60s was confirmed dead at George Washington University Hospital with a gunshot wound to the head.
One employee, who declined to be identified, told The Washington Post he heard "blam, blam" inside one of the buildings, then someone pulled the fire alarm.
"We still don't know all the facts, but we do know that several people have been shot, and some have been killed," President Barack Obama said Monday before remarks to mark the fifth anniversary of the financial crisis. "So we are confronting yet another mass shooting -- and today, it happened on a military installation in our nation's capital. ...
"We send our thoughts and prayers to all at the Navy Yard who've been touched by this tragedy. We will do everything in our power to make sure whoever carried out this cowardly act is held responsible."
Police said family members were directed to nearby Nationals Stadium parking lot B to meet up with Navy Yard employees who were allowed to leave the complex.
"Family members look