Patricia Ward, a logistics management specialist at the Navy Yard, said she heard a series of shots, at least seven, in rapid succession.
"A few of us just ran outside the side exit," Ward said.
Outside the building she saw a security guard with her gun drawn who told them to run and shelter.
Ward said the building has security.
"You need a card to enter the building. It's very hard to get in without a card," she said.
"Being with the incident that happened today, not secure enough for me," Ward said.
Frank Putzo, an attorney at the Navy Yard, told ABC News affiliate WJLA-TV he was on the fourth floor of the building when the shooting began.
"We heard three sounds, it sounded like a table collapsing on the ground," he said.
He said he came out of his office and heard a "very loud pop" about a minute later that he estimated was about 100 feet away.
"When that happened everyone said, 'This is no drill, go, go, go,'" he said. "And a whole bunch of us were able to make it to the emergency exits. And we heard several more shots."
The Naval Sea Systems Command, the largest of the Navy's five commands, is responsible for engineering, building, buying and maintaining ships, submarines and combat systems in the Navy's fleet.