A Navy officer who was inside the complex told CNN people scrambled for cover after hearing someone shout to get out of the building and stay away from the cafeteria.
But Lieutenant Commander Scott Williams said he heard no shots or saw any signs of a struggle.
"We heard someone scream, get out of the building, stay away from the cafeteria and we saw everyone running for the exits or adjoining offices," he said.
"NavyYard Lockdown/shelter continues. No further info at this time. More to follow," it said.
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Police cars converged on the scene in southeast Washington, and television images showed a huge traffic jam outside the complex.
Authorities stepped up security outside the White House, closing the pedestrian mall that runs along Pennsylvania Avenue and the adjoining Lafayette Square.
The Navy Yard was the scene of a September 2013 shooting that saw a lone gunman fatally shoot 12 people before being killed himself in a shootout with police.
The incident comes with the United States on heightened alert ahead of the July 4 national holiday.
The FBI, Department of Homeland Security and National Counterterrorism Center have warned the public of an increased risk of attack during Independence Day weekend.